T cell data

mypairs(dat_mapped[,c(glue("Day15{c(rbind(S1[1:2], S2[1:2]))}"))], gap=0)

tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("Day15{S1[i]}")]]), !is.na(dat_mapped[[glue("Day15{S2[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1)
tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON          686    0    0  576
## cd4_IFNg.IL2_BA.4.5            691   12    2  557
## cd8_IFNg.IL2_COV2.CON          686    0    1  575
## cd8_IFNg.IL2_BA.4.5            691   12    4  555
## cd4_IFNg.IL2.154_COV2.CON      686    0    0  576
## cd4_IFNg.IL2.154_BA.4.5        691   12    2  557
## cd4_IL4.IL5.IL13.154_COV2.CON  686    0    0  576
## cd4_IL4.IL5.IL13.154_BA.4.5    691   12    2  557
## cd4_IL21_COV2.CON              686    0    0  576
## cd4_IL21_BA.4.5                691   12    2  557
## cd4_IFNg_COV2.CON              686    0    0  576
## cd4_IFNg_BA.4.5                691   12    2  557
## cd4_IL2_COV2.CON               686    0    0  576
## cd4_IL2_BA.4.5                 691   12    2  557
## cd4_TNFa_COV2.CON              686    0    0  576
## cd4_TNFa_BA.4.5                691   12    2  557
## cd8_IFNg_COV2.CON              686    0    1  575
## cd8_IFNg_BA.4.5                691   12    4  555
## cd8_IL2_COV2.CON               686    0    1  575
## cd8_IL2_BA.4.5                 691   12    4  555
## cd8_TNFa_COV2.CON              686    0    1  575
## cd8_TNFa_BA.4.5                691   12    4  555
## cd4_154_COV2.CON               686    0    0  576
## cd4_154_BA.4.5                 691   12    2  557
## cd4_IL17a_COV2.CON             686    0    0  576
## cd4_IL17a_BA.4.5               691   12    2  557
## cd4_IL4.154_COV2.CON           686    0    0  576
## cd4_IL4.154_BA.4.5             691   12    2  557
## cd4_IL5.IL13.154_COV2.CON      686    0    0  576
## cd4_IL5.IL13.154_BA.4.5        691   12    2  557
## cd4_CXCR5.154_COV2.CON         686    0    1  575
## cd4_CXCR5.154_BA.4.5           694   12    7  549
## cd4_CXCR5.IL21_COV2.CON        686    0    1  575
## cd4_CXCR5.IL21_BA.4.5          694   12    7  549
## cd8_IFNg.IL2.TNFa_COV2.CON     686    0    1  575
## cd8_IFNg.IL2.TNFa_BA.4.5       691   12    4  555
i=2; mytable(!is.na(dat_mapped[[glue("Day15{S1[i]}")]]), !is.na(dat_mapped[[glue("Day15{S2[i]}")]]))
##        
##         FALSE TRUE
##   FALSE   691    2
##   TRUE     12  557
i=1; mytable(!is.na(dat_mapped[[glue("Day15{S1[i]}")]]), !is.na(dat_mapped[[glue("Day15{S2[i]}")]]), dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   598    0
##   TRUE      0  456
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    55    0
##   TRUE      0  107
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    33    0
##   TRUE      0   13
i=1; mytable(!is.na(dat_mapped[[glue("Day15{S2[i]}")]]), !is.na(dat_mapped[["Day15cd4_IFNg.IL2_Wuhan.N"]]), 
dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   598    0
##   TRUE     26  430
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    55    0
##   TRUE      5  102
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    33    0
##   TRUE      0   13
mytable(rowSums(!is.na(dat_mapped[glue("Day15{tcellvv}")])))
## 
##   0  36  54  72  85  86  88  90 
## 686   5  10  20   5   3  12 521
# t(dat_mapped[which(rowSums(!is.na(dat_mapped[glue("Day15{tcellvv}")]))==36),201:300])
mypairs(dat_mapped[,c(glue("B{c(rbind(S1[1:2], S2[1:2]))}"))], gap=0)

tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1)
tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON          686    0    0  576
## cd4_IFNg.IL2_BA.4.5            691   19    1  551
## cd8_IFNg.IL2_COV2.CON          686    0    0  576
## cd8_IFNg.IL2_BA.4.5            691   19    3  549
## cd4_IFNg.IL2.154_COV2.CON      686    0    0  576
## cd4_IFNg.IL2.154_BA.4.5        691   19    1  551
## cd4_IL4.IL5.IL13.154_COV2.CON  686    0    0  576
## cd4_IL4.IL5.IL13.154_BA.4.5    691   19    1  551
## cd4_IL21_COV2.CON              686    0    0  576
## cd4_IL21_BA.4.5                691   19    1  551
## cd4_IFNg_COV2.CON              686    0    0  576
## cd4_IFNg_BA.4.5                691   19    1  551
## cd4_IL2_COV2.CON               686    0    0  576
## cd4_IL2_BA.4.5                 691   19    1  551
## cd4_TNFa_COV2.CON              686    0    0  576
## cd4_TNFa_BA.4.5                691   19    1  551
## cd8_IFNg_COV2.CON              686    0    0  576
## cd8_IFNg_BA.4.5                691   19    3  549
## cd8_IL2_COV2.CON               686    0    0  576
## cd8_IL2_BA.4.5                 691   19    3  549
## cd8_TNFa_COV2.CON              686    0    0  576
## cd8_TNFa_BA.4.5                691   19    3  549
## cd4_154_COV2.CON               686    0    0  576
## cd4_154_BA.4.5                 691   19    1  551
## cd4_IL17a_COV2.CON             686    0    0  576
## cd4_IL17a_BA.4.5               691   19    1  551
## cd4_IL4.154_COV2.CON           686    0    0  576
## cd4_IL4.154_BA.4.5             691   19    1  551
## cd4_IL5.IL13.154_COV2.CON      686    0    0  576
## cd4_IL5.IL13.154_BA.4.5        691   19    1  551
## cd4_CXCR5.154_COV2.CON         686    0    1  575
## cd4_CXCR5.154_BA.4.5           694   19    6  543
## cd4_CXCR5.IL21_COV2.CON        686    0    1  575
## cd4_CXCR5.IL21_BA.4.5          694   19    6  543
## cd8_IFNg.IL2.TNFa_COV2.CON     686    0    0  576
## cd8_IFNg.IL2.TNFa_BA.4.5       691   19    3  549
i=2; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]))
##        
##         FALSE TRUE
##   FALSE   691    1
##   TRUE     19  551
i=1; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]), dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   598    0
##   TRUE      0  456
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    54    0
##   TRUE      0  108
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    34    0
##   TRUE      0   12
i=1; mytable(!is.na(dat_mapped[[glue("B{S2[i]}")]]), !is.na(dat_mapped[["Day15cd4_IFNg.IL2_Wuhan.N"]]), 
dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   592    6
##   TRUE     32  424
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    54    0
##   TRUE      6  102
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    33    1
##   TRUE      0   12
mytable(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")])))
## 
##   0  36  54  72  85  86  88  90 
## 686   5  18  38   3   3  11 498
t(dat_mapped[which(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")]))==36),201:300])
##                                           188         306         541
## Bcd4_CXCR5.IL21_BA.4.5.S2                  NA          NA          NA
## Bcd4_CXCR5.IL21_COV2.CON.S1       0.014437157 0.004467056 0.001000000
## Bcd4_CXCR5.IL21_COV2.CON.S2       0.001000000 0.001000000 0.001000000
## Bcd4_CXCR5.IL21_Wuhan.N                    NA          NA          NA
## Bcd4_IFNg_BA.4.5.S1                        NA          NA          NA
## Bcd4_IFNg_BA.4.5.S2                        NA          NA          NA
## Bcd4_IFNg_COV2.CON.S1             0.231073038 0.049872446 0.089807106
## Bcd4_IFNg_COV2.CON.S2             0.131226468 0.043148201 0.103975807
## Bcd4_IFNg_Wuhan.N                          NA          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S1                    NA          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S2                    NA          NA          NA
## Bcd4_IFNg.IL2_COV2.CON.S1         0.368800537 0.071189236 0.082697693
## Bcd4_IFNg.IL2_COV2.CON.S2         0.238105378 0.065693293 0.099041092
## Bcd4_IFNg.IL2_Wuhan.N                      NA          NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S1                NA          NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S2                NA          NA          NA
## Bcd4_IFNg.IL2.154_COV2.CON.S1     0.418913129 0.074412217 0.082763326
## Bcd4_IFNg.IL2.154_COV2.CON.S2     0.264305574 0.076316213 0.100689069
## Bcd4_IFNg.IL2.154_Wuhan.N                  NA          NA          NA
## Bcd4_IL17a_BA.4.5.S1                       NA          NA          NA
## Bcd4_IL17a_BA.4.5.S2                       NA          NA          NA
## Bcd4_IL17a_COV2.CON.S1            0.004124902 0.001000000 0.004358710
## Bcd4_IL17a_COV2.CON.S2            0.003980733 0.003144674 0.010688086
## Bcd4_IL17a_Wuhan.N                         NA          NA          NA
## Bcd4_IL2_BA.4.5.S1                         NA          NA          NA
## Bcd4_IL2_BA.4.5.S2                         NA          NA          NA
## Bcd4_IL2_COV2.CON.S1              0.269267644 0.063424004 0.038801777
## Bcd4_IL2_COV2.CON.S2              0.185892686 0.061919684 0.050058636
## Bcd4_IL2_Wuhan.N                           NA          NA          NA
## Bcd4_IL21_BA.4.5.S1                        NA          NA          NA
## Bcd4_IL21_BA.4.5.S2                        NA          NA          NA
## Bcd4_IL21_COV2.CON.S1             0.076389212 0.007690037 0.050302716
## Bcd4_IL21_COV2.CON.S2             0.009814104 0.003759814 0.054059757
## Bcd4_IL21_Wuhan.N                          NA          NA          NA
## Bcd4_IL4.154_BA.4.5.S1                     NA          NA          NA
## Bcd4_IL4.154_BA.4.5.S2                     NA          NA          NA
## Bcd4_IL4.154_COV2.CON.S1          0.001000000 0.001000000 0.001000000
## Bcd4_IL4.154_COV2.CON.S2          0.001000000 0.001000000 0.001000000
## Bcd4_IL4.154_Wuhan.N                       NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S1            NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S2            NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S1 0.001000000 0.001903710 0.001000000
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S2 0.001000000 0.001873010 0.001000000
## Bcd4_IL4.IL5.IL13.154_Wuhan.N              NA          NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S1                NA          NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S2                NA          NA          NA
## Bcd4_IL5.IL13.154_COV2.CON.S1     0.001000000 0.001903710 0.001000000
## Bcd4_IL5.IL13.154_COV2.CON.S2     0.001990367 0.001873010 0.001000000
## Bcd4_IL5.IL13.154_Wuhan.N                  NA          NA          NA
## Bcd4_TNFa_BA.4.5.S1                        NA          NA          NA
## Bcd4_TNFa_BA.4.5.S2                        NA          NA          NA
## Bcd4_TNFa_COV2.CON.S1             0.355526818 0.001000000 0.001000000
## Bcd4_TNFa_COV2.CON.S2             0.253389639 0.001000000 0.001000000
## Bcd4_TNFa_Wuhan.N                          NA          NA          NA
## Bcd8_IFNg_BA.4.5.S1                        NA          NA          NA
## Bcd8_IFNg_BA.4.5.S2                        NA          NA          NA
## Bcd8_IFNg_COV2.CON.S1             0.004075968 0.001000000 0.017488870
## Bcd8_IFNg_COV2.CON.S2             0.006330431 0.003894445 0.001000000
## Bcd8_IFNg_Wuhan.N                          NA          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S1                    NA          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S2                    NA          NA          NA
## Bcd8_IFNg.IL2_COV2.CON.S1         0.004075968 0.001000000 0.033458209
## Bcd8_IFNg.IL2_COV2.CON.S2         0.008633358 0.003894445 0.012971951
## Bcd8_IFNg.IL2_Wuhan.N                      NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S1               NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S2               NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S1    0.010023720 0.001000000 0.005209820
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S2    0.014532644 0.005627565 0.001000000
## Bcd8_IFNg.IL2.TNFa_Wuhan.N                 NA          NA          NA
## Bcd8_IL2_BA.4.5.S1                         NA          NA          NA
## Bcd8_IL2_BA.4.5.S2                         NA          NA          NA
## Bcd8_IL2_COV2.CON.S1              0.001000000 0.001000000 0.008201745
## Bcd8_IL2_COV2.CON.S2              0.002302927 0.001000000 0.029646354
## Bcd8_IL2_Wuhan.N                           NA          NA          NA
## Bcd8_TNFa_BA.4.5.S1                        NA          NA          NA
## Bcd8_TNFa_BA.4.5.S2                        NA          NA          NA
## Bcd8_TNFa_COV2.CON.S1             0.005947751 0.001000000 0.012760338
## Bcd8_TNFa_COV2.CON.S2             0.008202214 0.001000000 0.001000000
## Bcd8_TNFa_Wuhan.N                          NA          NA          NA
## Day15cd4_154_BA.4.5.S1            0.670446287 0.138362130 0.093446034
## Day15cd4_154_BA.4.5.S2            0.441614813          NA 0.074328671
## Day15cd4_154_COV2.CON.S1          0.732183666 0.180064972 0.128435391
## Day15cd4_154_COV2.CON.S2          0.424804333 0.193484068 0.089379914
## Day15cd4_154_Wuhan.N              0.039243080          NA 0.073720925
## Day15cd4_CXCR5.154_BA.4.5.S1      0.038345029 0.018148994 0.004033772
## Day15cd4_CXCR5.154_BA.4.5.S2      0.023400806          NA 0.006143236
## Day15cd4_CXCR5.154_COV2.CON.S1    0.032358148 0.033012250 0.006973130
## Day15cd4_CXCR5.154_COV2.CON.S2    0.008763167 0.024092413 0.008965998
## Day15cd4_CXCR5.154_Wuhan.N        0.006753563          NA 0.011745836
## Day15cd4_CXCR5.IL21_BA.4.5.S1     0.021089766 0.002865631 0.001000000
## Day15cd4_CXCR5.IL21_BA.4.5.S2     0.011700403          NA 0.002546184
## Day15cd4_CXCR5.IL21_COV2.CON.S1   0.013323943 0.007074054 0.001086433
## Day15cd4_CXCR5.IL21_COV2.CON.S2   0.003505267 0.010144174 0.001721183
## Day15cd4_CXCR5.IL21_Wuhan.N       0.001688391          NA 0.001743479
## Day15cd4_IFNg_BA.4.5.S1           0.568500577 0.112581012 0.097479806
## Day15cd4_IFNg_BA.4.5.S2           0.346254485          NA 0.071617099
## Day15cd4_IFNg_COV2.CON.S1         0.651922454 0.146838480 0.126505564
## Day15cd4_IFNg_COV2.CON.S2         0.333500633 0.171624443 0.097445311
## Day15cd4_IFNg_Wuhan.N             0.042517337          NA 0.065530917
## Day15cd4_IFNg.IL2_BA.4.5.S1       0.710377183 0.151553499 0.096430692
##                                           542         546
## Bcd4_CXCR5.IL21_BA.4.5.S2                  NA          NA
## Bcd4_CXCR5.IL21_COV2.CON.S1       0.003822271 0.001000000
## Bcd4_CXCR5.IL21_COV2.CON.S2       0.001000000 0.001000000
## Bcd4_CXCR5.IL21_Wuhan.N                    NA          NA
## Bcd4_IFNg_BA.4.5.S1                        NA          NA
## Bcd4_IFNg_BA.4.5.S2                        NA          NA
## Bcd4_IFNg_COV2.CON.S1             0.069755310 0.030218373
## Bcd4_IFNg_COV2.CON.S2             0.125680722 0.039321171
## Bcd4_IFNg_Wuhan.N                          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S1                    NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S2                    NA          NA
## Bcd4_IFNg.IL2_COV2.CON.S1         0.116576996 0.023255226
## Bcd4_IFNg.IL2_COV2.CON.S2         0.224547861 0.051406264
## Bcd4_IFNg.IL2_Wuhan.N                      NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S1                NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S2                NA          NA
## Bcd4_IFNg.IL2.154_COV2.CON.S1     0.129272234 0.025418511
## Bcd4_IFNg.IL2.154_COV2.CON.S2     0.233485722 0.051406264
## Bcd4_IFNg.IL2.154_Wuhan.N                  NA          NA
## Bcd4_IL17a_BA.4.5.S1                       NA          NA
## Bcd4_IL17a_BA.4.5.S2                       NA          NA
## Bcd4_IL17a_COV2.CON.S1            0.001000000 0.002095672
## Bcd4_IL17a_COV2.CON.S2            0.002012079 0.001000000
## Bcd4_IL17a_Wuhan.N                         NA          NA
## Bcd4_IL2_BA.4.5.S1                         NA          NA
## Bcd4_IL2_BA.4.5.S2                         NA          NA
## Bcd4_IL2_COV2.CON.S1              0.108898207 0.012506416
## Bcd4_IL2_COV2.CON.S2              0.188351643 0.043743813
## Bcd4_IL2_Wuhan.N                           NA          NA
## Bcd4_IL21_BA.4.5.S1                        NA          NA
## Bcd4_IL21_BA.4.5.S2                        NA          NA
## Bcd4_IL21_COV2.CON.S1             0.003073321 0.001000000
## Bcd4_IL21_COV2.CON.S2             0.003134613 0.001000000
## Bcd4_IL21_Wuhan.N                          NA          NA
## Bcd4_IL4.154_BA.4.5.S1                     NA          NA
## Bcd4_IL4.154_BA.4.5.S2                     NA          NA
## Bcd4_IL4.154_COV2.CON.S1          0.001000000 0.001000000
## Bcd4_IL4.154_COV2.CON.S2          0.001000000 0.001978670
## Bcd4_IL4.154_Wuhan.N                       NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S1            NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S2            NA          NA
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S1 0.001000000 0.001000000
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S2 0.001000000 0.001000000
## Bcd4_IL4.IL5.IL13.154_Wuhan.N              NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S1                NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S2                NA          NA
## Bcd4_IL5.IL13.154_COV2.CON.S1     0.001000000 0.001000000
## Bcd4_IL5.IL13.154_COV2.CON.S2     0.001000000 0.001000000
## Bcd4_IL5.IL13.154_Wuhan.N                  NA          NA
## Bcd4_TNFa_BA.4.5.S1                        NA          NA
## Bcd4_TNFa_BA.4.5.S2                        NA          NA
## Bcd4_TNFa_COV2.CON.S1             0.087647264 0.001000000
## Bcd4_TNFa_COV2.CON.S2             0.169840571 0.001000000
## Bcd4_TNFa_Wuhan.N                          NA          NA
## Bcd8_IFNg_BA.4.5.S1                        NA          NA
## Bcd8_IFNg_BA.4.5.S2                        NA          NA
## Bcd8_IFNg_COV2.CON.S1             0.025910547 0.019815029
## Bcd8_IFNg_COV2.CON.S2             0.145304185 0.032749356
## Bcd8_IFNg_Wuhan.N                          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S1                    NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S2                    NA          NA
## Bcd8_IFNg.IL2_COV2.CON.S1         0.022343196 0.016886600
## Bcd8_IFNg.IL2_COV2.CON.S2         0.159070861 0.029820927
## Bcd8_IFNg.IL2_Wuhan.N                      NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S1               NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S2               NA          NA
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S1    0.022718830 0.022563465
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S2    0.144801454 0.029182500
## Bcd8_IFNg.IL2.TNFa_Wuhan.N                 NA          NA
## Bcd8_IL2_BA.4.5.S1                         NA          NA
## Bcd8_IL2_BA.4.5.S2                         NA          NA
## Bcd8_IL2_COV2.CON.S1              0.003849077 0.001000000
## Bcd8_IL2_COV2.CON.S2              0.096869457 0.001000000
## Bcd8_IL2_Wuhan.N                           NA          NA
## Bcd8_TNFa_BA.4.5.S1                        NA          NA
## Bcd8_TNFa_BA.4.5.S2                        NA          NA
## Bcd8_TNFa_COV2.CON.S1             0.022718830 0.028672314
## Bcd8_TNFa_COV2.CON.S2             0.127467427 0.017519679
## Bcd8_TNFa_Wuhan.N                          NA          NA
## Day15cd4_154_BA.4.5.S1            0.099916638 0.101356502
## Day15cd4_154_BA.4.5.S2            0.246679127 0.089917283
## Day15cd4_154_COV2.CON.S1          0.143497231 0.083196271
## Day15cd4_154_COV2.CON.S2          0.236429577 0.100542189
## Day15cd4_154_Wuhan.N              0.001000000 0.011245048
## Day15cd4_CXCR5.154_BA.4.5.S1      0.012290861 0.001911096
## Day15cd4_CXCR5.154_BA.4.5.S2      0.043487000 0.003336726
## Day15cd4_CXCR5.154_COV2.CON.S1    0.017738435 0.003865407
## Day15cd4_CXCR5.154_COV2.CON.S2    0.036133347 0.005295769
## Day15cd4_CXCR5.154_Wuhan.N        0.001000000 0.001000000
## Day15cd4_CXCR5.IL21_BA.4.5.S1     0.001000000 0.005801711
## Day15cd4_CXCR5.IL21_BA.4.5.S2     0.003143008 0.003162416
## Day15cd4_CXCR5.IL21_COV2.CON.S1   0.005689719 0.001000000
## Day15cd4_CXCR5.IL21_COV2.CON.S2   0.009385890 0.001687840
## Day15cd4_CXCR5.IL21_Wuhan.N       0.002376547 0.001000000
## Day15cd4_IFNg_BA.4.5.S1           0.070479141 0.097465887
## Day15cd4_IFNg_BA.4.5.S2           0.175513422 0.105106859
## Day15cd4_IFNg_COV2.CON.S1         0.106430611 0.085038944
## Day15cd4_IFNg_COV2.CON.S2         0.194794945 0.125333192
## Day15cd4_IFNg_Wuhan.N             0.001000000 0.011451755
## Day15cd4_IFNg.IL2_BA.4.5.S1       0.104366912 0.110911981
# cross-tabulate missingness between baseline and D15
tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("Day15{S1[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1); tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON          679    7    7  569
## cd4_IFNg.IL2_BA.4.5            679   14   13  556
## cd8_IFNg.IL2_COV2.CON          679    8    7  568
## cd8_IFNg.IL2_BA.4.5            681   14   13  554
## cd4_IFNg.IL2.154_COV2.CON      679    7    7  569
## cd4_IFNg.IL2.154_BA.4.5        679   14   13  556
## cd4_IL4.IL5.IL13.154_COV2.CON  679    7    7  569
## cd4_IL4.IL5.IL13.154_BA.4.5    679   14   13  556
## cd4_IL21_COV2.CON              679    7    7  569
## cd4_IL21_BA.4.5                679   14   13  556
## cd4_IFNg_COV2.CON              679    7    7  569
## cd4_IFNg_BA.4.5                679   14   13  556
## cd4_IL2_COV2.CON               679    7    7  569
## cd4_IL2_BA.4.5                 679   14   13  556
## cd4_TNFa_COV2.CON              679    7    7  569
## cd4_TNFa_BA.4.5                679   14   13  556
## cd8_IFNg_COV2.CON              679    8    7  568
## cd8_IFNg_BA.4.5                681   14   13  554
## cd8_IL2_COV2.CON               679    8    7  568
## cd8_IL2_BA.4.5                 681   14   13  554
## cd8_TNFa_COV2.CON              679    8    7  568
## cd8_TNFa_BA.4.5                681   14   13  554
## cd4_154_COV2.CON               679    7    7  569
## cd4_154_BA.4.5                 679   14   13  556
## cd4_IL17a_COV2.CON             679    7    7  569
## cd4_IL17a_BA.4.5               679   14   13  556
## cd4_IL4.154_COV2.CON           679    7    7  569
## cd4_IL4.154_BA.4.5             679   14   13  556
## cd4_IL5.IL13.154_COV2.CON      679    7    7  569
## cd4_IL5.IL13.154_BA.4.5        679   14   13  556
## cd4_CXCR5.154_COV2.CON         680    7    7  568
## cd4_CXCR5.154_BA.4.5           687   14   13  548
## cd4_CXCR5.IL21_COV2.CON        680    7    7  568
## cd4_CXCR5.IL21_BA.4.5          687   14   13  548
## cd8_IFNg.IL2.TNFa_COV2.CON     679    8    7  568
## cd8_IFNg.IL2.TNFa_BA.4.5       681   14   13  554
mypairs(dat_mapped[,c(glue("B{c(rbind(S1[1:2]))}"), glue("Day15{c(rbind(S1[1:2]))}"))], gap=0)

mypairs(log10(dat_mapped[,c(glue("Day91{c(rbind(S1[1:2], S2[1:2]))}"))]), gap=0)

tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("Day91{S1[i]}")]]), !is.na(dat_mapped[[glue("Day91{S2[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1)
tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON         1088    0    0  174
## cd4_IFNg.IL2_BA.4.5           1091    3    1  167
## cd8_IFNg.IL2_COV2.CON         1088    0    0  174
## cd8_IFNg.IL2_BA.4.5           1091    3    2  166
## cd4_IFNg.IL2.154_COV2.CON     1088    0    0  174
## cd4_IFNg.IL2.154_BA.4.5       1091    3    1  167
## cd4_IL4.IL5.IL13.154_COV2.CON 1088    0    0  174
## cd4_IL4.IL5.IL13.154_BA.4.5   1091    3    1  167
## cd4_IL21_COV2.CON             1088    0    0  174
## cd4_IL21_BA.4.5               1091    3    1  167
## cd4_IFNg_COV2.CON             1088    0    0  174
## cd4_IFNg_BA.4.5               1091    3    1  167
## cd4_IL2_COV2.CON              1088    0    0  174
## cd4_IL2_BA.4.5                1091    3    1  167
## cd4_TNFa_COV2.CON             1088    0    0  174
## cd4_TNFa_BA.4.5               1091    3    1  167
## cd8_IFNg_COV2.CON             1088    0    0  174
## cd8_IFNg_BA.4.5               1091    3    2  166
## cd8_IL2_COV2.CON              1088    0    0  174
## cd8_IL2_BA.4.5                1091    3    2  166
## cd8_TNFa_COV2.CON             1088    0    0  174
## cd8_TNFa_BA.4.5               1091    3    2  166
## cd4_154_COV2.CON              1088    0    0  174
## cd4_154_BA.4.5                1091    3    1  167
## cd4_IL17a_COV2.CON            1088    0    0  174
## cd4_IL17a_BA.4.5              1091    3    1  167
## cd4_IL4.154_COV2.CON          1088    0    0  174
## cd4_IL4.154_BA.4.5            1091    3    1  167
## cd4_IL5.IL13.154_COV2.CON     1088    0    0  174
## cd4_IL5.IL13.154_BA.4.5       1091    3    1  167
## cd4_CXCR5.154_COV2.CON        1088    0    0  174
## cd4_CXCR5.154_BA.4.5          1094    2    5  161
## cd4_CXCR5.IL21_COV2.CON       1088    0    0  174
## cd4_CXCR5.IL21_BA.4.5         1094    2    5  161
## cd8_IFNg.IL2.TNFa_COV2.CON    1088    0    0  174
## cd8_IFNg.IL2.TNFa_BA.4.5      1091    3    2  166
i=2; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]))
##        
##         FALSE TRUE
##   FALSE   691    1
##   TRUE     19  551
i=1; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]), dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   598    0
##   TRUE      0  456
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    54    0
##   TRUE      0  108
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    34    0
##   TRUE      0   12
i=1; mytable(!is.na(dat_mapped[[glue("B{S2[i]}")]]), !is.na(dat_mapped[["Day91cd4_IFNg.IL2_Wuhan.N"]]), 
dat_mapped$COVIDIndD22toD91)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   596    2
##   TRUE    335  121
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    54    0
##   TRUE     77   31
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    34    0
##   TRUE      9    3
mytable(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")])))
## 
##   0  36  54  72  85  86  88  90 
## 686   5  18  38   3   3  11 498
# t(dat_mapped[which(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")]))==36),201:300])

# cross-tabulate missingness between baseline and D91
tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("Day91{S1[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1); tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON          683  405    3  171
## cd4_IFNg.IL2_BA.4.5            688  404    4  166
## cd8_IFNg.IL2_COV2.CON          683  405    3  171
## cd8_IFNg.IL2_BA.4.5            690  403    4  165
## cd4_IFNg.IL2.154_COV2.CON      683  405    3  171
## cd4_IFNg.IL2.154_BA.4.5        688  404    4  166
## cd4_IL4.IL5.IL13.154_COV2.CON  683  405    3  171
## cd4_IL4.IL5.IL13.154_BA.4.5    688  404    4  166
## cd4_IL21_COV2.CON              683  405    3  171
## cd4_IL21_BA.4.5                688  404    4  166
## cd4_IFNg_COV2.CON              683  405    3  171
## cd4_IFNg_BA.4.5                688  404    4  166
## cd4_IL2_COV2.CON               683  405    3  171
## cd4_IL2_BA.4.5                 688  404    4  166
## cd4_TNFa_COV2.CON              683  405    3  171
## cd4_TNFa_BA.4.5                688  404    4  166
## cd8_IFNg_COV2.CON              683  405    3  171
## cd8_IFNg_BA.4.5                690  403    4  165
## cd8_IL2_COV2.CON               683  405    3  171
## cd8_IL2_BA.4.5                 690  403    4  165
## cd8_TNFa_COV2.CON              683  405    3  171
## cd8_TNFa_BA.4.5                690  403    4  165
## cd4_154_COV2.CON               683  405    3  171
## cd4_154_BA.4.5                 688  404    4  166
## cd4_IL17a_COV2.CON             683  405    3  171
## cd4_IL17a_BA.4.5               688  404    4  166
## cd4_IL4.154_COV2.CON           683  405    3  171
## cd4_IL4.154_BA.4.5             688  404    4  166
## cd4_IL5.IL13.154_COV2.CON      683  405    3  171
## cd4_IL5.IL13.154_BA.4.5        688  404    4  166
## cd4_CXCR5.154_COV2.CON         683  405    4  170
## cd4_CXCR5.154_BA.4.5           696  403    4  159
## cd4_CXCR5.IL21_COV2.CON        683  405    4  170
## cd4_CXCR5.IL21_BA.4.5          696  403    4  159
## cd8_IFNg.IL2.TNFa_COV2.CON     683  405    3  171
## cd8_IFNg.IL2.TNFa_BA.4.5       690  403    4  165
mypairs(log10(dat_mapped[,c(glue("B{c(rbind(S1[1:2]))}"), glue("Day91{c(rbind(S1[1:2]))}"))]), gap=0)

mypairs(log10(dat_mapped[,c(glue("Day181{c(rbind(S1[1:2], S2[1:2]))}"))]), gap=0)

tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("Day181{S1[i]}")]]), !is.na(dat_mapped[[glue("Day181{S2[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1)
tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON         1123    0    0  139
## cd4_IFNg.IL2_BA.4.5           1127    4    1  130
## cd8_IFNg.IL2_COV2.CON         1123    0    0  139
## cd8_IFNg.IL2_BA.4.5           1127    4    2  129
## cd4_IFNg.IL2.154_COV2.CON     1123    0    0  139
## cd4_IFNg.IL2.154_BA.4.5       1127    4    1  130
## cd4_IL4.IL5.IL13.154_COV2.CON 1123    0    0  139
## cd4_IL4.IL5.IL13.154_BA.4.5   1127    4    1  130
## cd4_IL21_COV2.CON             1123    0    0  139
## cd4_IL21_BA.4.5               1127    4    1  130
## cd4_IFNg_COV2.CON             1123    0    0  139
## cd4_IFNg_BA.4.5               1127    4    1  130
## cd4_IL2_COV2.CON              1123    0    0  139
## cd4_IL2_BA.4.5                1127    4    1  130
## cd4_TNFa_COV2.CON             1123    0    0  139
## cd4_TNFa_BA.4.5               1127    4    1  130
## cd8_IFNg_COV2.CON             1123    0    0  139
## cd8_IFNg_BA.4.5               1127    4    2  129
## cd8_IL2_COV2.CON              1123    0    0  139
## cd8_IL2_BA.4.5                1127    4    2  129
## cd8_TNFa_COV2.CON             1123    0    0  139
## cd8_TNFa_BA.4.5               1127    4    2  129
## cd4_154_COV2.CON              1123    0    0  139
## cd4_154_BA.4.5                1127    4    1  130
## cd4_IL17a_COV2.CON            1123    0    0  139
## cd4_IL17a_BA.4.5              1127    4    1  130
## cd4_IL4.154_COV2.CON          1123    0    0  139
## cd4_IL4.154_BA.4.5            1127    4    1  130
## cd4_IL5.IL13.154_COV2.CON     1123    0    0  139
## cd4_IL5.IL13.154_BA.4.5       1127    4    1  130
## cd4_CXCR5.154_COV2.CON        1123    0    0  139
## cd4_CXCR5.154_BA.4.5          1127    4    1  130
## cd4_CXCR5.IL21_COV2.CON       1123    0    0  139
## cd4_CXCR5.IL21_BA.4.5         1127    4    1  130
## cd8_IFNg.IL2.TNFa_COV2.CON    1123    0    0  139
## cd8_IFNg.IL2.TNFa_BA.4.5      1127    4    2  129
i=2; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]))
##        
##         FALSE TRUE
##   FALSE   691    1
##   TRUE     19  551
i=1; mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("B{S2[i]}")]]), dat_mapped$COVIDIndD22toD181)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   576    0
##   TRUE      0  404
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    76    0
##   TRUE      0  160
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    34    0
##   TRUE      0   12
i=1; mytable(!is.na(dat_mapped[[glue("B{S2[i]}")]]), !is.na(dat_mapped[["Day181cd4_IFNg.IL2_Wuhan.N"]]), 
dat_mapped$COVIDIndD22toD181)
## , ,  = 0
## 
##        
##         FALSE TRUE
##   FALSE   573    3
##   TRUE    298  106
## 
## , ,  = 1
## 
##        
##         FALSE TRUE
##   FALSE    76    0
##   TRUE    144   16
## 
## , ,  = NA
## 
##        
##         FALSE TRUE
##   FALSE    34    0
##   TRUE     12    0
mytable(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")])))
## 
##   0  36  54  72  85  86  88  90 
## 686   5  18  38   3   3  11 498
t(dat_mapped[which(rowSums(!is.na(dat_mapped[glue("B{tcellvv}")]))==36),201:300])
##                                           188         306         541
## Bcd4_CXCR5.IL21_BA.4.5.S2                  NA          NA          NA
## Bcd4_CXCR5.IL21_COV2.CON.S1       0.014437157 0.004467056 0.001000000
## Bcd4_CXCR5.IL21_COV2.CON.S2       0.001000000 0.001000000 0.001000000
## Bcd4_CXCR5.IL21_Wuhan.N                    NA          NA          NA
## Bcd4_IFNg_BA.4.5.S1                        NA          NA          NA
## Bcd4_IFNg_BA.4.5.S2                        NA          NA          NA
## Bcd4_IFNg_COV2.CON.S1             0.231073038 0.049872446 0.089807106
## Bcd4_IFNg_COV2.CON.S2             0.131226468 0.043148201 0.103975807
## Bcd4_IFNg_Wuhan.N                          NA          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S1                    NA          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S2                    NA          NA          NA
## Bcd4_IFNg.IL2_COV2.CON.S1         0.368800537 0.071189236 0.082697693
## Bcd4_IFNg.IL2_COV2.CON.S2         0.238105378 0.065693293 0.099041092
## Bcd4_IFNg.IL2_Wuhan.N                      NA          NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S1                NA          NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S2                NA          NA          NA
## Bcd4_IFNg.IL2.154_COV2.CON.S1     0.418913129 0.074412217 0.082763326
## Bcd4_IFNg.IL2.154_COV2.CON.S2     0.264305574 0.076316213 0.100689069
## Bcd4_IFNg.IL2.154_Wuhan.N                  NA          NA          NA
## Bcd4_IL17a_BA.4.5.S1                       NA          NA          NA
## Bcd4_IL17a_BA.4.5.S2                       NA          NA          NA
## Bcd4_IL17a_COV2.CON.S1            0.004124902 0.001000000 0.004358710
## Bcd4_IL17a_COV2.CON.S2            0.003980733 0.003144674 0.010688086
## Bcd4_IL17a_Wuhan.N                         NA          NA          NA
## Bcd4_IL2_BA.4.5.S1                         NA          NA          NA
## Bcd4_IL2_BA.4.5.S2                         NA          NA          NA
## Bcd4_IL2_COV2.CON.S1              0.269267644 0.063424004 0.038801777
## Bcd4_IL2_COV2.CON.S2              0.185892686 0.061919684 0.050058636
## Bcd4_IL2_Wuhan.N                           NA          NA          NA
## Bcd4_IL21_BA.4.5.S1                        NA          NA          NA
## Bcd4_IL21_BA.4.5.S2                        NA          NA          NA
## Bcd4_IL21_COV2.CON.S1             0.076389212 0.007690037 0.050302716
## Bcd4_IL21_COV2.CON.S2             0.009814104 0.003759814 0.054059757
## Bcd4_IL21_Wuhan.N                          NA          NA          NA
## Bcd4_IL4.154_BA.4.5.S1                     NA          NA          NA
## Bcd4_IL4.154_BA.4.5.S2                     NA          NA          NA
## Bcd4_IL4.154_COV2.CON.S1          0.001000000 0.001000000 0.001000000
## Bcd4_IL4.154_COV2.CON.S2          0.001000000 0.001000000 0.001000000
## Bcd4_IL4.154_Wuhan.N                       NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S1            NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S2            NA          NA          NA
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S1 0.001000000 0.001903710 0.001000000
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S2 0.001000000 0.001873010 0.001000000
## Bcd4_IL4.IL5.IL13.154_Wuhan.N              NA          NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S1                NA          NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S2                NA          NA          NA
## Bcd4_IL5.IL13.154_COV2.CON.S1     0.001000000 0.001903710 0.001000000
## Bcd4_IL5.IL13.154_COV2.CON.S2     0.001990367 0.001873010 0.001000000
## Bcd4_IL5.IL13.154_Wuhan.N                  NA          NA          NA
## Bcd4_TNFa_BA.4.5.S1                        NA          NA          NA
## Bcd4_TNFa_BA.4.5.S2                        NA          NA          NA
## Bcd4_TNFa_COV2.CON.S1             0.355526818 0.001000000 0.001000000
## Bcd4_TNFa_COV2.CON.S2             0.253389639 0.001000000 0.001000000
## Bcd4_TNFa_Wuhan.N                          NA          NA          NA
## Bcd8_IFNg_BA.4.5.S1                        NA          NA          NA
## Bcd8_IFNg_BA.4.5.S2                        NA          NA          NA
## Bcd8_IFNg_COV2.CON.S1             0.004075968 0.001000000 0.017488870
## Bcd8_IFNg_COV2.CON.S2             0.006330431 0.003894445 0.001000000
## Bcd8_IFNg_Wuhan.N                          NA          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S1                    NA          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S2                    NA          NA          NA
## Bcd8_IFNg.IL2_COV2.CON.S1         0.004075968 0.001000000 0.033458209
## Bcd8_IFNg.IL2_COV2.CON.S2         0.008633358 0.003894445 0.012971951
## Bcd8_IFNg.IL2_Wuhan.N                      NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S1               NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S2               NA          NA          NA
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S1    0.010023720 0.001000000 0.005209820
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S2    0.014532644 0.005627565 0.001000000
## Bcd8_IFNg.IL2.TNFa_Wuhan.N                 NA          NA          NA
## Bcd8_IL2_BA.4.5.S1                         NA          NA          NA
## Bcd8_IL2_BA.4.5.S2                         NA          NA          NA
## Bcd8_IL2_COV2.CON.S1              0.001000000 0.001000000 0.008201745
## Bcd8_IL2_COV2.CON.S2              0.002302927 0.001000000 0.029646354
## Bcd8_IL2_Wuhan.N                           NA          NA          NA
## Bcd8_TNFa_BA.4.5.S1                        NA          NA          NA
## Bcd8_TNFa_BA.4.5.S2                        NA          NA          NA
## Bcd8_TNFa_COV2.CON.S1             0.005947751 0.001000000 0.012760338
## Bcd8_TNFa_COV2.CON.S2             0.008202214 0.001000000 0.001000000
## Bcd8_TNFa_Wuhan.N                          NA          NA          NA
## Day15cd4_154_BA.4.5.S1            0.670446287 0.138362130 0.093446034
## Day15cd4_154_BA.4.5.S2            0.441614813          NA 0.074328671
## Day15cd4_154_COV2.CON.S1          0.732183666 0.180064972 0.128435391
## Day15cd4_154_COV2.CON.S2          0.424804333 0.193484068 0.089379914
## Day15cd4_154_Wuhan.N              0.039243080          NA 0.073720925
## Day15cd4_CXCR5.154_BA.4.5.S1      0.038345029 0.018148994 0.004033772
## Day15cd4_CXCR5.154_BA.4.5.S2      0.023400806          NA 0.006143236
## Day15cd4_CXCR5.154_COV2.CON.S1    0.032358148 0.033012250 0.006973130
## Day15cd4_CXCR5.154_COV2.CON.S2    0.008763167 0.024092413 0.008965998
## Day15cd4_CXCR5.154_Wuhan.N        0.006753563          NA 0.011745836
## Day15cd4_CXCR5.IL21_BA.4.5.S1     0.021089766 0.002865631 0.001000000
## Day15cd4_CXCR5.IL21_BA.4.5.S2     0.011700403          NA 0.002546184
## Day15cd4_CXCR5.IL21_COV2.CON.S1   0.013323943 0.007074054 0.001086433
## Day15cd4_CXCR5.IL21_COV2.CON.S2   0.003505267 0.010144174 0.001721183
## Day15cd4_CXCR5.IL21_Wuhan.N       0.001688391          NA 0.001743479
## Day15cd4_IFNg_BA.4.5.S1           0.568500577 0.112581012 0.097479806
## Day15cd4_IFNg_BA.4.5.S2           0.346254485          NA 0.071617099
## Day15cd4_IFNg_COV2.CON.S1         0.651922454 0.146838480 0.126505564
## Day15cd4_IFNg_COV2.CON.S2         0.333500633 0.171624443 0.097445311
## Day15cd4_IFNg_Wuhan.N             0.042517337          NA 0.065530917
## Day15cd4_IFNg.IL2_BA.4.5.S1       0.710377183 0.151553499 0.096430692
##                                           542         546
## Bcd4_CXCR5.IL21_BA.4.5.S2                  NA          NA
## Bcd4_CXCR5.IL21_COV2.CON.S1       0.003822271 0.001000000
## Bcd4_CXCR5.IL21_COV2.CON.S2       0.001000000 0.001000000
## Bcd4_CXCR5.IL21_Wuhan.N                    NA          NA
## Bcd4_IFNg_BA.4.5.S1                        NA          NA
## Bcd4_IFNg_BA.4.5.S2                        NA          NA
## Bcd4_IFNg_COV2.CON.S1             0.069755310 0.030218373
## Bcd4_IFNg_COV2.CON.S2             0.125680722 0.039321171
## Bcd4_IFNg_Wuhan.N                          NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S1                    NA          NA
## Bcd4_IFNg.IL2_BA.4.5.S2                    NA          NA
## Bcd4_IFNg.IL2_COV2.CON.S1         0.116576996 0.023255226
## Bcd4_IFNg.IL2_COV2.CON.S2         0.224547861 0.051406264
## Bcd4_IFNg.IL2_Wuhan.N                      NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S1                NA          NA
## Bcd4_IFNg.IL2.154_BA.4.5.S2                NA          NA
## Bcd4_IFNg.IL2.154_COV2.CON.S1     0.129272234 0.025418511
## Bcd4_IFNg.IL2.154_COV2.CON.S2     0.233485722 0.051406264
## Bcd4_IFNg.IL2.154_Wuhan.N                  NA          NA
## Bcd4_IL17a_BA.4.5.S1                       NA          NA
## Bcd4_IL17a_BA.4.5.S2                       NA          NA
## Bcd4_IL17a_COV2.CON.S1            0.001000000 0.002095672
## Bcd4_IL17a_COV2.CON.S2            0.002012079 0.001000000
## Bcd4_IL17a_Wuhan.N                         NA          NA
## Bcd4_IL2_BA.4.5.S1                         NA          NA
## Bcd4_IL2_BA.4.5.S2                         NA          NA
## Bcd4_IL2_COV2.CON.S1              0.108898207 0.012506416
## Bcd4_IL2_COV2.CON.S2              0.188351643 0.043743813
## Bcd4_IL2_Wuhan.N                           NA          NA
## Bcd4_IL21_BA.4.5.S1                        NA          NA
## Bcd4_IL21_BA.4.5.S2                        NA          NA
## Bcd4_IL21_COV2.CON.S1             0.003073321 0.001000000
## Bcd4_IL21_COV2.CON.S2             0.003134613 0.001000000
## Bcd4_IL21_Wuhan.N                          NA          NA
## Bcd4_IL4.154_BA.4.5.S1                     NA          NA
## Bcd4_IL4.154_BA.4.5.S2                     NA          NA
## Bcd4_IL4.154_COV2.CON.S1          0.001000000 0.001000000
## Bcd4_IL4.154_COV2.CON.S2          0.001000000 0.001978670
## Bcd4_IL4.154_Wuhan.N                       NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S1            NA          NA
## Bcd4_IL4.IL5.IL13.154_BA.4.5.S2            NA          NA
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S1 0.001000000 0.001000000
## Bcd4_IL4.IL5.IL13.154_COV2.CON.S2 0.001000000 0.001000000
## Bcd4_IL4.IL5.IL13.154_Wuhan.N              NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S1                NA          NA
## Bcd4_IL5.IL13.154_BA.4.5.S2                NA          NA
## Bcd4_IL5.IL13.154_COV2.CON.S1     0.001000000 0.001000000
## Bcd4_IL5.IL13.154_COV2.CON.S2     0.001000000 0.001000000
## Bcd4_IL5.IL13.154_Wuhan.N                  NA          NA
## Bcd4_TNFa_BA.4.5.S1                        NA          NA
## Bcd4_TNFa_BA.4.5.S2                        NA          NA
## Bcd4_TNFa_COV2.CON.S1             0.087647264 0.001000000
## Bcd4_TNFa_COV2.CON.S2             0.169840571 0.001000000
## Bcd4_TNFa_Wuhan.N                          NA          NA
## Bcd8_IFNg_BA.4.5.S1                        NA          NA
## Bcd8_IFNg_BA.4.5.S2                        NA          NA
## Bcd8_IFNg_COV2.CON.S1             0.025910547 0.019815029
## Bcd8_IFNg_COV2.CON.S2             0.145304185 0.032749356
## Bcd8_IFNg_Wuhan.N                          NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S1                    NA          NA
## Bcd8_IFNg.IL2_BA.4.5.S2                    NA          NA
## Bcd8_IFNg.IL2_COV2.CON.S1         0.022343196 0.016886600
## Bcd8_IFNg.IL2_COV2.CON.S2         0.159070861 0.029820927
## Bcd8_IFNg.IL2_Wuhan.N                      NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S1               NA          NA
## Bcd8_IFNg.IL2.TNFa_BA.4.5.S2               NA          NA
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S1    0.022718830 0.022563465
## Bcd8_IFNg.IL2.TNFa_COV2.CON.S2    0.144801454 0.029182500
## Bcd8_IFNg.IL2.TNFa_Wuhan.N                 NA          NA
## Bcd8_IL2_BA.4.5.S1                         NA          NA
## Bcd8_IL2_BA.4.5.S2                         NA          NA
## Bcd8_IL2_COV2.CON.S1              0.003849077 0.001000000
## Bcd8_IL2_COV2.CON.S2              0.096869457 0.001000000
## Bcd8_IL2_Wuhan.N                           NA          NA
## Bcd8_TNFa_BA.4.5.S1                        NA          NA
## Bcd8_TNFa_BA.4.5.S2                        NA          NA
## Bcd8_TNFa_COV2.CON.S1             0.022718830 0.028672314
## Bcd8_TNFa_COV2.CON.S2             0.127467427 0.017519679
## Bcd8_TNFa_Wuhan.N                          NA          NA
## Day15cd4_154_BA.4.5.S1            0.099916638 0.101356502
## Day15cd4_154_BA.4.5.S2            0.246679127 0.089917283
## Day15cd4_154_COV2.CON.S1          0.143497231 0.083196271
## Day15cd4_154_COV2.CON.S2          0.236429577 0.100542189
## Day15cd4_154_Wuhan.N              0.001000000 0.011245048
## Day15cd4_CXCR5.154_BA.4.5.S1      0.012290861 0.001911096
## Day15cd4_CXCR5.154_BA.4.5.S2      0.043487000 0.003336726
## Day15cd4_CXCR5.154_COV2.CON.S1    0.017738435 0.003865407
## Day15cd4_CXCR5.154_COV2.CON.S2    0.036133347 0.005295769
## Day15cd4_CXCR5.154_Wuhan.N        0.001000000 0.001000000
## Day15cd4_CXCR5.IL21_BA.4.5.S1     0.001000000 0.005801711
## Day15cd4_CXCR5.IL21_BA.4.5.S2     0.003143008 0.003162416
## Day15cd4_CXCR5.IL21_COV2.CON.S1   0.005689719 0.001000000
## Day15cd4_CXCR5.IL21_COV2.CON.S2   0.009385890 0.001687840
## Day15cd4_CXCR5.IL21_Wuhan.N       0.002376547 0.001000000
## Day15cd4_IFNg_BA.4.5.S1           0.070479141 0.097465887
## Day15cd4_IFNg_BA.4.5.S2           0.175513422 0.105106859
## Day15cd4_IFNg_COV2.CON.S1         0.106430611 0.085038944
## Day15cd4_IFNg_COV2.CON.S2         0.194794945 0.125333192
## Day15cd4_IFNg_Wuhan.N             0.001000000 0.011451755
## Day15cd4_IFNg.IL2_BA.4.5.S1       0.104366912 0.110911981
# cross-tabulate missingness between baseline and D181
tab=mysapply (1:length(S1), function(i) {
  c(mytable(!is.na(dat_mapped[[glue("B{S1[i]}")]]), !is.na(dat_mapped[[glue("Day181{S1[i]}")]])))
})
rownames(tab)=sub(".S1", "", S1); tab
##                               [,1] [,2] [,3] [,4]
## cd4_IFNg.IL2_COV2.CON          683  440    3  136
## cd4_IFNg.IL2_BA.4.5            688  440    4  130
## cd8_IFNg.IL2_COV2.CON          683  440    3  136
## cd8_IFNg.IL2_BA.4.5            690  439    4  129
## cd4_IFNg.IL2.154_COV2.CON      683  440    3  136
## cd4_IFNg.IL2.154_BA.4.5        688  440    4  130
## cd4_IL4.IL5.IL13.154_COV2.CON  683  440    3  136
## cd4_IL4.IL5.IL13.154_BA.4.5    688  440    4  130
## cd4_IL21_COV2.CON              683  440    3  136
## cd4_IL21_BA.4.5                688  440    4  130
## cd4_IFNg_COV2.CON              683  440    3  136
## cd4_IFNg_BA.4.5                688  440    4  130
## cd4_IL2_COV2.CON               683  440    3  136
## cd4_IL2_BA.4.5                 688  440    4  130
## cd4_TNFa_COV2.CON              683  440    3  136
## cd4_TNFa_BA.4.5                688  440    4  130
## cd8_IFNg_COV2.CON              683  440    3  136
## cd8_IFNg_BA.4.5                690  439    4  129
## cd8_IL2_COV2.CON               683  440    3  136
## cd8_IL2_BA.4.5                 690  439    4  129
## cd8_TNFa_COV2.CON              683  440    3  136
## cd8_TNFa_BA.4.5                690  439    4  129
## cd4_154_COV2.CON               683  440    3  136
## cd4_154_BA.4.5                 688  440    4  130
## cd4_IL17a_COV2.CON             683  440    3  136
## cd4_IL17a_BA.4.5               688  440    4  130
## cd4_IL4.154_COV2.CON           683  440    3  136
## cd4_IL4.154_BA.4.5             688  440    4  130
## cd4_IL5.IL13.154_COV2.CON      683  440    3  136
## cd4_IL5.IL13.154_BA.4.5        688  440    4  130
## cd4_CXCR5.154_COV2.CON         683  440    4  135
## cd4_CXCR5.154_BA.4.5           696  432    4  130
## cd4_CXCR5.IL21_COV2.CON        683  440    4  135
## cd4_CXCR5.IL21_BA.4.5          696  432    4  130
## cd8_IFNg.IL2.TNFa_COV2.CON     683  440    3  136
## cd8_IFNg.IL2.TNFa_BA.4.5       690  439    4  129
mypairs(dat_mapped[,c(glue("B{c(rbind(S1[1:2]))}"), glue("Day181{c(rbind(S1[1:2]))}"))], gap=0)

explore the second order effect

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ FOIstandardized + standardized_risk_score + scale(Bpseudoneutid50_MDW, scale=F) + I(scale(Day15pseudoneutid50_MDW, scale=F)^2) + scale(Day15pseudoneutid50_MDW, scale=F), subset(dat, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     FOIstandardized + standardized_risk_score + scale(Bpseudoneutid50_MDW, 
##         scale = F) + I(scale(Day15pseudoneutid50_MDW, scale = F)^2) + 
##         scale(Day15pseudoneutid50_MDW, scale = F), data = subset(dat, 
##     naive == 1))
## 
##                                                    coef exp(coef) se(coef)
## FOIstandardized                                -0.07363   0.92902  0.09311
## standardized_risk_score                         0.27288   1.31374  0.09695
## scale(Bpseudoneutid50_MDW, scale = F)          -0.36342   0.69530  0.17576
## I(scale(Day15pseudoneutid50_MDW, scale = F)^2) -0.88931   0.41094  0.30418
## scale(Day15pseudoneutid50_MDW, scale = F)      -0.12800   0.87985  0.24588
##                                                     z       p
## FOIstandardized                                -0.791 0.42908
## standardized_risk_score                         2.815 0.00488
## scale(Bpseudoneutid50_MDW, scale = F)          -2.068 0.03867
## I(scale(Day15pseudoneutid50_MDW, scale = F)^2) -2.924 0.00346
## scale(Day15pseudoneutid50_MDW, scale = F)      -0.521 0.60266
## 
## Likelihood ratio test=26.07  on 5 df, p=8.656e-05
## n= 629, number of events= 181
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ scale(Bpseudoneutid50_MDW, scale=F) + I(scale(Day15pseudoneutid50_MDW, scale=F)^2) + scale(Day15pseudoneutid50_MDW, scale=F), subset(dat, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     scale(Bpseudoneutid50_MDW, scale = F) + I(scale(Day15pseudoneutid50_MDW, 
##         scale = F)^2) + scale(Day15pseudoneutid50_MDW, scale = F), 
##     data = subset(dat, naive == 1))
## 
##                                                   coef exp(coef) se(coef)
## scale(Bpseudoneutid50_MDW, scale = F)          -0.2898    0.7484   0.1741
## I(scale(Day15pseudoneutid50_MDW, scale = F)^2) -0.8976    0.4075   0.3036
## scale(Day15pseudoneutid50_MDW, scale = F)      -0.1913    0.8259   0.2443
##                                                     z       p
## scale(Bpseudoneutid50_MDW, scale = F)          -1.664 0.09604
## I(scale(Day15pseudoneutid50_MDW, scale = F)^2) -2.957 0.00311
## scale(Day15pseudoneutid50_MDW, scale = F)      -0.783 0.43363
## 
## Likelihood ratio test=17.69  on 3 df, p=0.00051
## n= 629, number of events= 181
plot(Day15pseudoneutid50_MDW~Bpseudoneutid50_MDW, subset(dat, naive==1), col=subset(dat, naive==1)$COVIDIndD22toD181+1)

plot(Day15pseudoneutid50_MDW~Bpseudoneutid50_MDW, subset(dat, naive==0), col=subset(dat, naive==0)$COVIDIndD22toD181+1)

scatterplot of D15 and B

plot_anc_BA1=function(tmp, main) {
  par(mfrow=c(1,2), oma=c(0,2.5,3,0.5), mar=c(3,0,2,0), mgp = c(2, .5, 0))
  lim=c(0,4.5)
  
  plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp, col=ifelse(tmp$naive==1,1,2), main="Ancestral ID50", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
  plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp, col=ifelse(tmp$naive==1,1,2), main="BA1 ID50", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
  title(ylab="D15 (IU/ml)", outer=T, line=1.5)
  
  title(main=main, outer=T, line=0)
}

BA1 DI50 in one row and Ancestral ID50 in second row, three columns for three vaccines

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
    "1 Dose Prototype (Moderna)" # 50 ug
 ,  "1 Dose Omicron (Moderna)" # BA1
 , "Beta (Sanofi)", "Beta + Prototype (Sanofi)", "Prototype (Sanofi)"
  )
))
tmp$col=ifelse(tmp$naive==1,1,2); lim=c(0,4.5)
par(mfrow=c(2,3), oma=c(2.5,3.5,3,0.5), mar=c(0,0,2,0), mgp = c(2, .5, 0))

kp=tmp$treatment_assigned=="1 Dose Prototype (Moderna)";                                              plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Moderna Prototype", line=1)
kp=tmp$treatment_assigned=="1 Dose Omicron (Moderna)";                                                plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Moderna BA.1", line=1)
kp=tmp$treatment_assigned %in% c("Beta (Sanofi)", "Beta + Prototype (Sanofi)", "Prototype (Sanofi)"); plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Sanofi", line=1)

par(mar=c(0,0,0,0))
kp=tmp$treatment_assigned=="1 Dose Prototype (Moderna)";                                              plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
kp=tmp$treatment_assigned=="1 Dose Omicron (Moderna)";                                                plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
kp=tmp$treatment_assigned %in% c("Beta (Sanofi)", "Beta + Prototype (Sanofi)", "Prototype (Sanofi)"); plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)

title(ylab="Ancestral ID50                              BA.1 ID50", outer=T, line=2.5, font.lab=2)
title(ylab="D15 (IU/ml)", outer=T, line=1.5)
title(xlab="D1 (IU/ml)", outer=T, line=1.5) 

COVAIL Sanofi

tmp=convert2IU(dat.sanofi)
plot_anc_BA1(tmp, main="COVAIL Sanofi")

Three Sanofi arms plotted separately

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
 "Beta (Sanofi)", "Beta + Prototype (Sanofi)", "Prototype (Sanofi)"
  )
))
tmp$col=ifelse(tmp$naive==1,1,2); lim=c(0,4.5)
par(mfrow=c(2,3), oma=c(2.5,3.5,3,0.5), mar=c(0,0,2,0), mgp = c(2, .5, 0))

kp=tmp$treatment_assigned %in% c("Prototype (Sanofi)"); plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Prototype", line=1)
kp=tmp$treatment_assigned=="Beta (Sanofi)";             plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Beta", line=1)
kp=tmp$treatment_assigned=="Beta + Prototype (Sanofi)"; plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1); title(main="Prototype + Beta", line=1)

par(mar=c(0,0,0,0))
kp=tmp$treatment_assigned %in% c("Prototype (Sanofi)"); plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
kp=tmp$treatment_assigned=="Beta (Sanofi)";             plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
kp=tmp$treatment_assigned=="Beta + Prototype (Sanofi)"; plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp[kp,], col=tmp$col[kp], main="", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)

title(ylab="Ancestral ID50                              BA.1 ID50", outer=T, line=2.5, font.lab=2)
title(ylab="D15 (IU/ml)", outer=T, line=1.5)
title(xlab="D1 (IU/ml)", outer=T, line=1.5) 
title(main="Sanoifi", outer=T, line=1.5) 

COVAIL moderna prototype

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
    "1 Dose Prototype (Moderna)" # 50 ug
  )
))
plot_anc_BA1(tmp, main="COVAIL Moderna Prototype (50ug)") # COVAIL mRNA-1273 Prototype Dose 4 (50ug)

COVAIL moderna Omicron BA1

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
  "1 Dose Omicron (Moderna)" # BA1
  )
))
plot_anc_BA1(tmp, main="COVAIL Moderna BA.1 (50ug)") # COVAIL mRNA-1273 BA.1 Dose 4 (50ug)

COVAIL moderna prototype and BA1 together

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
    "1 Dose Prototype (Moderna)" # 50 ug
   ,"1 Dose Omicron (Moderna)" # BA1
  )
))
tmp$trt=ifelse(tmp$treatment_assigned=="1 Dose Prototype (Moderna)",1,0)
main="COVAIL Moderna (50ug)"

par(mfrow=c(1,2), oma=c(0,2.5,3,0.5), mar=c(3,0,2,0), mgp = c(2, .5, 0))
lim=c(0,4.5)

plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp, pch=ifelse(tmp$naive==1,1,2), col=ifelse(tmp$trt==1,1,2), main="Ancestral ID50", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1,   tmp, pch=ifelse(tmp$naive==1,1,2), col=ifelse(tmp$trt==1,1,2), main="BA1 ID50", xlab="D1 (IU/ml)", xlim=lim, ylim=lim, asp=1); abline(0,1)
# mylegend(legend=c())

title(ylab="D15 (IU/ml)", outer=T, line=1.5)

title(main=main, outer=T, line=0)

COVAIL mRNA

tmp=convert2IU(dat.ocp)
plot_anc_BA1(tmp, main="COVAIL Omi/Prot 1 dose mRNA")

Cox model using a generated marker based on baseline

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
   "1 Dose Omicron (Moderna)" # BA1
)))

tmp1 = subset(tmp, Bpseudoneutid50_D614G>0.5 & Day15pseudoneutid50_D614G<4)

fit=lm(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G+I(Bpseudoneutid50_D614G^2)+I(Bpseudoneutid50_D614G^3), tmp1)

tmp$pred=predict(fit,newdata=tmp)
tmp$resid=tmp$Day15pseudoneutid50_D614G-tmp$pred
tmp1$pred=predict(fit,newdata=tmp1)

plot(Day15pseudoneutid50_D614G~Bpseudoneutid50_D614G, tmp, xlim=c(0,5), ylim=c(0,5), asp=1); mylines(tmp$Bpseudoneutid50_D614G, tmp$pred, col=2)

par(mfrow=c(1,2))
lim=NULL
corplot(Day15pseudoneutid50_D614G~resid, tmp, xlim=NULL, ylim=c(0,5), asp=1)
corplot(Bpseudoneutid50_D614G~resid, tmp, xlim=NULL, ylim=c(0,5), asp=1)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + Day15pseudoneutid50_D614G, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + Day15pseudoneutid50_D614G, data = tmp)
## 
##                              coef exp(coef) se(coef)      z      p
## naive                      1.9245    6.8514   1.0371  1.856 0.0635
## Day15pseudoneutid50_D614G -1.0112    0.3638   0.4784 -2.114 0.0345
## 
## Likelihood ratio test=14.4  on 2 df, p=0.0007468
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + Bpseudoneutid50_D614G, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + Bpseudoneutid50_D614G, data = tmp)
## 
##                          coef exp(coef) se(coef)      z      p
## naive                  2.0548    7.8054   1.0389  1.978 0.0479
## Bpseudoneutid50_D614G -0.3143    0.7303   0.3050 -1.031 0.3028
## 
## Likelihood ratio test=10.94  on 2 df, p=0.004209
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + pred, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + pred, data = tmp)
## 
##          coef exp(coef) se(coef)      z      p
## naive  2.2008    9.0320   1.0299  2.137 0.0326
## pred  -0.1359    0.8730   0.4590 -0.296 0.7673
## 
## Likelihood ratio test=10.01  on 2 df, p=0.006712
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + resid, data = tmp)
## 
##          coef exp(coef) se(coef)      z      p
## naive  2.1879    8.9161   1.0225  2.140 0.0324
## resid -1.4238    0.2408   0.7234 -1.968 0.0491
## 
## Likelihood ratio test=14.62  on 2 df, p=0.0006689
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ pred + resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     pred + resid, data = tmp)
## 
##          coef exp(coef) se(coef)      z      p
## pred  -1.1754    0.3087   0.5867 -2.003 0.0451
## resid -1.6826    0.1859   0.6816 -2.468 0.0136
## 
## Likelihood ratio test=8.85  on 2 df, p=0.01196
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ pred * resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     pred * resid, data = tmp)
## 
##                 coef exp(coef)  se(coef)      z      p
## pred       -1.158783  0.313868  0.668844 -1.733 0.0832
## resid      -4.788847  0.008322  7.790670 -0.615 0.5388
## pred:resid  1.073863  2.926663  2.564098  0.419 0.6754
## 
## Likelihood ratio test=9.24  on 3 df, p=0.02627
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Bpseudoneutid50_D614G + resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Bpseudoneutid50_D614G + resid, data = tmp)
## 
##                          coef exp(coef) se(coef)      z      p
## Bpseudoneutid50_D614G -0.8558    0.4249   0.3560 -2.404 0.0162
## resid                 -1.6077    0.2004   0.7080 -2.271 0.0232
## 
## Likelihood ratio test=11.28  on 2 df, p=0.003547
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Bpseudoneutid50_D614G * resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Bpseudoneutid50_D614G * resid, data = tmp)
## 
##                                coef exp(coef) se(coef)      z     p
## Bpseudoneutid50_D614G       -0.8440    0.4300   0.3656 -2.309 0.021
## resid                       -2.2611    0.1042   2.5370 -0.891 0.373
## Bpseudoneutid50_D614G:resid  0.3220    1.3799   1.1381  0.283 0.777
## 
## Likelihood ratio test=11.38  on 3 df, p=0.009818
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Day15pseudoneutid50_D614G + resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Day15pseudoneutid50_D614G + resid, data = tmp)
## 
##                              coef exp(coef) se(coef)      z      p
## Day15pseudoneutid50_D614G -1.1754    0.3087   0.5867 -2.003 0.0451
## resid                     -0.5072    0.6022   0.8296 -0.611 0.5410
## 
## Likelihood ratio test=8.85  on 2 df, p=0.01196
## n= 96, number of events= 25
# coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + Day15pseudoneutid50_D614G, tmp1)
# coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + pred, tmp1)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + Bpseudoneutid50_D614G * resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + Bpseudoneutid50_D614G * resid, data = tmp)
## 
##                                coef exp(coef) se(coef)      z      p
## naive                        1.8667    6.4668   1.0507  1.777 0.0756
## Bpseudoneutid50_D614G       -0.5178    0.5959   0.3842 -1.348 0.1778
## resid                       -2.0123    0.1337   2.5373 -0.793 0.4277
## Bpseudoneutid50_D614G:resid  0.3010    1.3513   1.1426  0.263 0.7922
## 
## Likelihood ratio test=16.55  on 4 df, p=0.00236
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive * resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive * resid, data = tmp)
## 
##                  coef exp(coef)  se(coef)      z      p
## naive        2.906515 18.292940  1.584661  1.834 0.0666
## resid       -5.713483  0.003301  3.799761 -1.504 0.1327
## naive:resid  4.446396 85.318940  3.867496  1.150 0.2503
## 
## Likelihood ratio test=15.99  on 3 df, p=0.001141
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ naive + pred + resid, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     naive + pred + resid, data = tmp)
## 
##          coef exp(coef) se(coef)      z      p
## naive  2.0212    7.5476   1.0399  1.944 0.0519
## pred  -0.6244    0.5356   0.6384 -0.978 0.3281
## resid -1.4546    0.2335   0.6894 -2.110 0.0349
## 
## Likelihood ratio test=15.51  on 3 df, p=0.001428
## n= 96, number of events= 25

repeat for BA1 marker. not significant

tmp=convert2IU(subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
   "1 Dose Omicron (Moderna)" # BA1
)))

fit=lm(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1+I(Bpseudoneutid50_BA.1^2), subset(tmp, Day15pseudoneutid50_BA.1>1))
tmp$pred=predict(fit,newdata=tmp)

plot(Day15pseudoneutid50_BA.1~Bpseudoneutid50_BA.1, tmp, xlim=c(0,5), ylim=c(0,5), asp=1); mylines(tmp$Bpseudoneutid50_BA.1, tmp$pred, col=2)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Day15pseudoneutid50_BA.1 + naive, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Day15pseudoneutid50_BA.1 + naive, data = tmp)
## 
##                             coef exp(coef) se(coef)      z      p
## Day15pseudoneutid50_BA.1 -0.3955    0.6733   0.2953 -1.339 0.1804
## naive                     2.0235    7.5650   1.0372  1.951 0.0511
## 
## Likelihood ratio test=11.53  on 2 df, p=0.003133
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Bpseudoneutid50_BA.1 + naive, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Bpseudoneutid50_BA.1 + naive, data = tmp)
## 
##                         coef exp(coef) se(coef)      z      p
## Bpseudoneutid50_BA.1 -0.4027    0.6685   0.2733 -1.473 0.1406
## naive                 1.8507    6.3645   1.0584  1.749 0.0804
## 
## Likelihood ratio test=12.14  on 2 df, p=0.002311
## n= 96, number of events= 25
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ pred + naive, tmp)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     pred + naive, data = tmp)
## 
##          coef exp(coef) se(coef)      z      p
## pred  -0.6858    0.5037   0.5333 -1.286 0.1985
## naive  1.9690    7.1639   1.0474  1.880 0.0601
## 
## Likelihood ratio test=11.55  on 2 df, p=0.003112
## n= 96, number of events= 25

For manuscript revision

compute median value for each category

tmp=subset(dat_proc, ph1.D15==1 & TrtonedosemRNA==1 & Day15pseudoneutid50_BA.1 <= 3.44762) # naive==1 & 
10**(wtd.quantile(tmp$Day15pseudoneutid50_BA.1, weights = tmp$wt.D15, probs = c(1/2)))
##    50% 
## 1358.5
tmp=subset(dat_proc, ph1.D15==1 & TrtonedosemRNA==1 & Day15pseudoneutid50_BA.1 > 3.44762 & Day15pseudoneutid50_BA.1 <= 3.95012) # & naive==1 
10**(wtd.quantile(tmp$Day15pseudoneutid50_BA.1, weights = tmp$wt.D15, probs = c(1/2)))
##      50% 
## 4830.996
tmp=subset(dat_proc, ph1.D15==1 & TrtonedosemRNA==1 & Day15pseudoneutid50_BA.1 > 3.95012) # & naive==1 
10**(wtd.quantile(tmp$Day15pseudoneutid50_BA.1, weights = tmp$wt.D15, probs = c(1/2)))
##   50% 
## 17121

Relationship between risk score and age

plot(dat_proc$Age, dat_proc$risk_score)

Difference in risk between prototype and Omicon vaccines

Summary: Between Pfz Prototype, Pfz Omicron, Mdn P, and Mdn O,

Risk is similar between Pfizer and Moderna in the prototype arms. Moderna P and O have similar risks, but Pfizer O has lower risk than P.

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ company, subset(dat.ocp,naive==1 & Trt==0))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     company, data = subset(dat.ocp, naive == 1 & Trt == 0))
## 
##              coef exp(coef) se(coef)     z     p
## companyPfz 0.4122    1.5101   0.3472 1.187 0.235
## 
## Likelihood ratio test=1.35  on 1 df, p=0.2454
## n= 105, number of events= 36
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + company + Day15pseudoneutid50_BA.4.BA.5 + FOIstandardized, subset(dat.ocp,naive==1 & Trt==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + company + Day15pseudoneutid50_BA.4.BA.5 + 
##         FOIstandardized, data = subset(dat.ocp, naive == 1 & 
##     Trt == 1))
## 
##                                  coef exp(coef) se(coef)      z        p
## standardized_risk_score        0.4680    1.5969   0.1666  2.810 0.004958
## companyPfz                    -0.9440    0.3891   0.3578 -2.638 0.008329
## Day15pseudoneutid50_BA.4.BA.5 -0.7299    0.4819   0.2006 -3.639 0.000273
## FOIstandardized               -0.1906    0.8264   0.2324 -0.820 0.412125
## 
## Likelihood ratio test=27.65  on 4 df, p=1.469e-05
## n= 213, number of events= 57
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt, subset(dat.ocp,naive==1 & company=="Pfz"))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt, data = subset(dat.ocp, naive == 1 & company == "Pfz"))
## 
##       coef exp(coef) se(coef)      z       p
## Trt -1.238     0.290    0.422 -2.933 0.00336
## 
## Likelihood ratio test=8.54  on 1 df, p=0.003482
## n= 98, number of events= 23
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt, subset(dat.ocp,naive==1 & company=="Mdn"))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt, data = subset(dat.ocp, naive == 1 & company == "Mdn"))
## 
##         coef exp(coef) se(coef)      z    p
## Trt -0.02566   0.97466  0.25475 -0.101 0.92
## 
## Likelihood ratio test=0.01  on 1 df, p=0.9199
## n= 220, number of events= 70
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt * company, subset(dat.ocp, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt * company, data = subset(dat.ocp, naive == 1))
## 
##                   coef exp(coef) se(coef)      z      p
## Trt            -0.0218    0.9784   0.2547 -0.086 0.9318
## companyPfz      0.4226    1.5259   0.3471  1.218 0.2234
## Trt:companyPfz -1.2309    0.2920   0.4917 -2.503 0.0123
## 
## Likelihood ratio test=10.39  on 3 df, p=0.01553
## n= 318, number of events= 93
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ I(1-Trt) * company, subset(dat.ocp, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     I(1 - Trt) * company, data = subset(dat.ocp, naive == 1))
## 
##                          coef exp(coef) se(coef)      z      p
## I(1 - Trt)             0.0218    1.0220   0.2547  0.086 0.9318
## companyPfz            -0.8083    0.4456   0.3483 -2.320 0.0203
## I(1 - Trt):companyPfz  1.2309    3.4242   0.4917  2.503 0.0123
## 
## Likelihood ratio test=10.39  on 3 df, p=0.01553
## n= 318, number of events= 93

Pfizer

OC v P is significant among the naive but not among the non-naive.

coxph(update(f, ~. + naive + Trt), dat.ocp.pfizer)
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = dat.ocp.pfizer)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.1126    0.8935   0.2984 -0.377 0.70591
## standardized_risk_score  0.2795    1.3224   0.2878  0.971 0.33154
## naive                    0.8310    2.2955   0.4551  1.826 0.06787
## Trt                     -1.1399    0.3199   0.3749 -3.040 0.00236
## 
## Likelihood ratio test=12.14  on 4 df, p=0.01631
## n= 151, number of events= 30
coxph(update(f, ~. + Trt), subset(dat.ocp.pfizer, naive==0))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.pfizer, 
##     naive == 0))
## 
##                             coef exp(coef) se(coef)      z     p
## FOIstandardized          0.59531   1.81359  0.61480  0.968 0.333
## standardized_risk_score  0.04664   1.04775  0.52826  0.088 0.930
## Trt                     -0.52997   0.58862  0.77255 -0.686 0.493
## 
## Likelihood ratio test=1.38  on 3 df, p=0.7098
## n= 53, number of events= 7
coxph(update(f, ~. + Trt), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.pfizer, 
##     naive == 1))
## 
##                            coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.3243    0.7231   0.3318 -0.977 0.3285
## standardized_risk_score  0.4130    1.5113   0.3592  1.150 0.2503
## Trt                     -1.3346    0.2633   0.4359 -3.062 0.0022
## 
## Likelihood ratio test=10.59  on 3 df, p=0.01415
## n= 98, number of events= 23
coxph(update(f, ~. + naive + Trt), dat.ocp.moderna)
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = dat.ocp.moderna)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.1298    0.8782   0.1923 -0.675 0.49956
## standardized_risk_score  0.2056    1.2283   0.1441  1.427 0.15360
## naive                    1.0871    2.9657   0.3741  2.906 0.00367
## Trt                     -0.1180    0.8887   0.2388 -0.494 0.62124
## 
## Likelihood ratio test=13.62  on 4 df, p=0.008612
## n= 284, number of events= 78
coxph(update(f, ~. + Trt), subset(dat.ocp.moderna, naive==0))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.moderna, 
##     naive == 0))
## 
##                            coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.4871    0.6144   0.5445 -0.895 0.3710
## standardized_risk_score -0.4855    0.6154   0.2100 -2.312 0.0208
## Trt                     -0.5147    0.5977   0.7306 -0.705 0.4811
## 
## Likelihood ratio test=6.87  on 3 df, p=0.07628
## n= 64, number of events= 8
coxph(update(f, ~. + Trt), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.moderna, 
##     naive == 1))
## 
##                             coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.03082   0.96965  0.20833 -0.148 0.8824
## standardized_risk_score  0.45535   1.57672  0.16296  2.794 0.0052
## Trt                     -0.07904   0.92400  0.25598 -0.309 0.7575
## 
## Likelihood ratio test=8.48  on 3 df, p=0.03705
## n= 220, number of events= 70
coxph(update(f, ~. + Trt), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.moderna, 
##     naive == 1))
## 
##                             coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.03082   0.96965  0.20833 -0.148 0.8824
## standardized_risk_score  0.45535   1.57672  0.16296  2.794 0.0052
## Trt                     -0.07904   0.92400  0.25598 -0.309 0.7575
## 
## Likelihood ratio test=8.48  on 3 df, p=0.03705
## n= 220, number of events= 70
coxph(update(f, ~. + Trt), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = update(f, ~. + Trt), data = subset(dat.ocp.pfizer, 
##     naive == 1))
## 
##                            coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.3243    0.7231   0.3318 -0.977 0.3285
## standardized_risk_score  0.4130    1.5113   0.3592  1.150 0.2503
## Trt                     -1.3346    0.2633   0.4359 -3.062 0.0022
## 
## Likelihood ratio test=10.59  on 3 df, p=0.01415
## n= 98, number of events= 23
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ I(1-Trt)*scale(standardized_risk_score), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     I(1 - Trt) * scale(standardized_risk_score), data = subset(dat.ocp.moderna, 
##     naive == 1))
## 
##                                              coef exp(coef) se(coef)      z
## I(1 - Trt)                                 0.1259    1.1341   0.2626  0.479
## scale(standardized_risk_score)             0.4569    1.5792   0.1567  2.917
## I(1 - Trt):scale(standardized_risk_score) -0.3079    0.7350   0.2860 -1.077
##                                                 p
## I(1 - Trt)                                0.63173
## scale(standardized_risk_score)            0.00354
## I(1 - Trt):scale(standardized_risk_score) 0.28163
## 
## Likelihood ratio test=9.58  on 3 df, p=0.02251
## n= 220, number of events= 70
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ I(1-Trt)*scale(standardized_risk_score), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     I(1 - Trt) * scale(standardized_risk_score), data = subset(dat.ocp.pfizer, 
##     naive == 1))
## 
##                                                coef exp(coef)  se(coef)      z
## I(1 - Trt)                                 1.334775  3.799141  0.439440  3.037
## scale(standardized_risk_score)             0.252246  1.286913  0.302894  0.833
## I(1 - Trt):scale(standardized_risk_score) -0.003043  0.996962  0.513319 -0.006
##                                                 p
## I(1 - Trt)                                0.00239
## scale(standardized_risk_score)            0.40496
## I(1 - Trt):scale(standardized_risk_score) 0.99527
## 
## Likelihood ratio test=9.64  on 3 df, p=0.02186
## n= 98, number of events= 23

D15 marker

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ I(1-Trt)*scale(standardized_risk_score) + I(1-Trt)*scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     I(1 - Trt) * scale(standardized_risk_score) + I(1 - Trt) * 
##         scale(Day15pseudoneutid50_BA.4.BA.5), data = subset(dat.ocp.moderna, 
##     naive == 1))
## 
##                                                    coef exp(coef) se(coef)
## I(1 - Trt)                                       0.1114    1.1178   0.2661
## scale(standardized_risk_score)                   0.4149    1.5142   0.1504
## scale(Day15pseudoneutid50_BA.4.BA.5)            -0.4160    0.6597   0.1256
## I(1 - Trt):scale(standardized_risk_score)       -0.2653    0.7670   0.2835
## I(1 - Trt):scale(Day15pseudoneutid50_BA.4.BA.5)  0.4191    1.5206   0.2328
##                                                      z        p
## I(1 - Trt)                                       0.419 0.675561
## scale(standardized_risk_score)                   2.759 0.005804
## scale(Day15pseudoneutid50_BA.4.BA.5)            -3.311 0.000929
## I(1 - Trt):scale(standardized_risk_score)       -0.936 0.349342
## I(1 - Trt):scale(Day15pseudoneutid50_BA.4.BA.5)  1.801 0.071746
## 
## Likelihood ratio test=19.05  on 5 df, p=0.001884
## n= 220, number of events= 70
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ I(1-Trt)*scale(standardized_risk_score) + I(1-Trt)*scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     I(1 - Trt) * scale(standardized_risk_score) + I(1 - Trt) * 
##         scale(Day15pseudoneutid50_BA.4.BA.5), data = subset(dat.ocp.pfizer, 
##     naive == 1))
## 
##                                                     coef exp(coef) se(coef)
## I(1 - Trt)                                       1.22319   3.39801  0.47177
## scale(standardized_risk_score)                   0.25727   1.29339  0.28060
## scale(Day15pseudoneutid50_BA.4.BA.5)            -0.39649   0.67268  0.30594
## I(1 - Trt):scale(standardized_risk_score)       -0.07131   0.93117  0.51280
## I(1 - Trt):scale(Day15pseudoneutid50_BA.4.BA.5)  0.08472   1.08841  0.48874
##                                                      z       p
## I(1 - Trt)                                       2.593 0.00952
## scale(standardized_risk_score)                   0.917 0.35923
## scale(Day15pseudoneutid50_BA.4.BA.5)            -1.296 0.19498
## I(1 - Trt):scale(standardized_risk_score)       -0.139 0.88940
## I(1 - Trt):scale(Day15pseudoneutid50_BA.4.BA.5)  0.173 0.86239
## 
## Likelihood ratio test=11.86  on 5 df, p=0.03673
## n= 98, number of events= 23
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt*scale(standardized_risk_score) + Trt*scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt * scale(standardized_risk_score) + Trt * scale(Day15pseudoneutid50_BA.4.BA.5), 
##     data = subset(dat.ocp.moderna, naive == 1))
## 
##                                               coef exp(coef)  se(coef)      z
## Trt                                      -0.111365  0.894612  0.266089 -0.419
## scale(standardized_risk_score)            0.149640  1.161417  0.240360  0.623
## scale(Day15pseudoneutid50_BA.4.BA.5)      0.003167  1.003172  0.195995  0.016
## Trt:scale(standardized_risk_score)        0.265277  1.303791  0.283455  0.936
## Trt:scale(Day15pseudoneutid50_BA.4.BA.5) -0.419130  0.657619  0.232756 -1.801
##                                               p
## Trt                                      0.6756
## scale(standardized_risk_score)           0.5336
## scale(Day15pseudoneutid50_BA.4.BA.5)     0.9871
## Trt:scale(standardized_risk_score)       0.3493
## Trt:scale(Day15pseudoneutid50_BA.4.BA.5) 0.0717
## 
## Likelihood ratio test=19.05  on 5 df, p=0.001884
## n= 220, number of events= 70
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt*scale(standardized_risk_score) + Trt*scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt * scale(standardized_risk_score) + Trt * scale(Day15pseudoneutid50_BA.4.BA.5), 
##     data = subset(dat.ocp.pfizer, naive == 1))
## 
##                                              coef exp(coef) se(coef)      z
## Trt                                      -1.22319   0.29429  0.47177 -2.593
## scale(standardized_risk_score)            0.18595   1.20437  0.42922  0.433
## scale(Day15pseudoneutid50_BA.4.BA.5)     -0.31177   0.73215  0.38065 -0.819
## Trt:scale(standardized_risk_score)        0.07131   1.07392  0.51280  0.139
## Trt:scale(Day15pseudoneutid50_BA.4.BA.5) -0.08472   0.91877  0.48874 -0.173
##                                                p
## Trt                                      0.00952
## scale(standardized_risk_score)           0.66484
## scale(Day15pseudoneutid50_BA.4.BA.5)     0.41276
## Trt:scale(standardized_risk_score)       0.88940
## Trt:scale(Day15pseudoneutid50_BA.4.BA.5) 0.86239
## 
## Likelihood ratio test=11.86  on 5 df, p=0.03673
## n= 98, number of events= 23
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt*scale(standardized_risk_score) + scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt * scale(standardized_risk_score) + scale(Day15pseudoneutid50_BA.4.BA.5), 
##     data = subset(dat.ocp.moderna, naive == 1))
## 
##                                          coef exp(coef) se(coef)      z       p
## Trt                                   0.01104   1.01111  0.26824  0.041 0.96716
## scale(standardized_risk_score)        0.19188   1.21152  0.23255  0.825 0.40932
## scale(Day15pseudoneutid50_BA.4.BA.5) -0.27822   0.75713  0.10780 -2.581 0.00986
## Trt:scale(standardized_risk_score)    0.23881   1.26974  0.27919  0.855 0.39234
## 
## Likelihood ratio test=15.7  on 4 df, p=0.003451
## n= 220, number of events= 70
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ Trt+scale(standardized_risk_score) + scale(Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp.pfizer, naive==1))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     Trt + scale(standardized_risk_score) + scale(Day15pseudoneutid50_BA.4.BA.5), 
##     data = subset(dat.ocp.pfizer, naive == 1))
## 
##                                         coef exp(coef) se(coef)      z       p
## Trt                                  -1.1912    0.3039   0.4390 -2.713 0.00666
## scale(standardized_risk_score)        0.2285    1.2567   0.2312  0.988 0.32313
## scale(Day15pseudoneutid50_BA.4.BA.5) -0.3558    0.7006   0.2317 -1.536 0.12463
## 
## Likelihood ratio test=11.81  on 3 df, p=0.008078
## n= 98, number of events= 23

BA4BA5-specific ID50 is significant correlate but not ancestral ID50.

coxph(update(f, ~. + Trt * Bpseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt * Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                                   coef exp(coef) se(coef)      z     p
## FOIstandardized               -0.37008   0.69068  0.32778 -1.129 0.259
## standardized_risk_score        0.46192   1.58712  0.35856  1.288 0.198
## Trt                           -1.45196   0.23411  1.39782 -1.039 0.299
## Bpseudoneutid50_BA.4.BA.5     -0.76476   0.46545  0.51612 -1.482 0.138
## Trt:Bpseudoneutid50_BA.4.BA.5  0.02565   1.02598  0.75166  0.034 0.973
## 
## Likelihood ratio test=14.86  on 5 df, p=0.011
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                              coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.3707    0.6903   0.3275 -1.132 0.25778
## standardized_risk_score    0.4619    1.5871   0.3584  1.289 0.19754
## Trt                       -1.4067    0.2449   0.4402 -3.196 0.00139
## Bpseudoneutid50_BA.4.BA.5 -0.7528    0.4711   0.3771 -1.996 0.04593
## 
## Likelihood ratio test=14.85  on 4 df, p=0.005012
## n= 98, number of events= 23
coxph(update(f, ~. + Trt * Day15pseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt * Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                                      coef exp(coef) se(coef)      z     p
## FOIstandardized                   -0.3928    0.6751   0.3376 -1.163 0.245
## standardized_risk_score            0.4077    1.5033   0.3387  1.204 0.229
## Trt                               -0.5003    0.6063   2.3862 -0.210 0.834
## Day15pseudoneutid50_BA.4.BA.5     -0.5345    0.5860   0.6290 -0.850 0.395
## Trt:Day15pseudoneutid50_BA.4.BA.5 -0.2392    0.7873   0.8374 -0.286 0.775
## 
## Likelihood ratio test=13.19  on 5 df, p=0.0217
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                                  coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.3846    0.6807   0.3365 -1.143 0.25298
## standardized_risk_score        0.3880    1.4741   0.3346  1.160 0.24613
## Trt                           -1.1710    0.3101   0.4380 -2.673 0.00751
## Day15pseudoneutid50_BA.4.BA.5 -0.6690    0.5122   0.4026 -1.661 0.09662
## 
## Likelihood ratio test=13.1  on 4 df, p=0.01078
## n= 98, number of events= 23
coxph(update(f, ~. + Trt * Bpseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt * Bpseudoneutid50_D614G), 
##     data = dat.1)
## 
##                              coef exp(coef) se(coef)      z     p
## FOIstandardized           -0.3129    0.7313   0.3325 -0.941 0.347
## standardized_risk_score    0.3846    1.4690   0.3593  1.070 0.284
## Trt                       -2.5917    0.0749   3.0261 -0.856 0.392
## Bpseudoneutid50_D614G     -0.7526    0.4711   0.6990 -1.077 0.282
## Trt:Bpseudoneutid50_D614G  0.3747    1.4545   0.9066  0.413 0.679
## 
## Likelihood ratio test=12.25  on 5 df, p=0.03156
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G), 
##     data = dat.1)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.3433    0.7094   0.3265 -1.051 0.29307
## standardized_risk_score  0.4042    1.4981   0.3542  1.141 0.25378
## Trt                     -1.3536    0.2583   0.4357 -3.106 0.00189
## Bpseudoneutid50_D614G   -0.5220    0.5934   0.4159 -1.255 0.20949
## 
## Likelihood ratio test=12.07  on 4 df, p=0.01682
## n= 98, number of events= 23
coxph(update(f, ~. + Trt * Day15pseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt * Day15pseudoneutid50_D614G), 
##     data = dat.1)
## 
##                                   coef exp(coef) se(coef)      z     p
## FOIstandardized               -0.34880   0.70554  0.33352 -1.046 0.296
## standardized_risk_score        0.37937   1.46136  0.33824  1.122 0.262
## Trt                            2.10109   8.17504  5.09592  0.412 0.680
## Day15pseudoneutid50_D614G      0.06733   1.06965  0.98947  0.068 0.946
## Trt:Day15pseudoneutid50_D614G -0.81890   0.44092  1.22190 -0.670 0.503
## 
## Likelihood ratio test=11.66  on 5 df, p=0.03977
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Day15pseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_D614G), 
##     data = dat.1)
## 
##                              coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.3568    0.6999   0.3320 -1.075 0.28252
## standardized_risk_score    0.3775    1.4586   0.3485  1.083 0.27878
## Trt                       -1.3000    0.2725   0.4364 -2.979 0.00289
## Day15pseudoneutid50_D614G -0.4664    0.6273   0.5907 -0.789 0.42983
## 
## Likelihood ratio test=11.21  on 4 df, p=0.02432
## n= 98, number of events= 23

Distribution of D15 BA4BA5-specific ID50 is different between P and OC

par(mfrow=c(1,2))
myboxplot(Bpseudoneutid50_BA.4.BA.5~Trt, dat.1, test="w")
myboxplot(Day15pseudoneutid50_BA.4.BA.5~Trt, dat.1, test="w")

Additional marker models

coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G + Day15pseudoneutid50_D614G + I(Day15pseudoneutid50_D614G^2)), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G + 
##     Day15pseudoneutid50_D614G + I(Day15pseudoneutid50_D614G^2)), 
##     data = dat.1)
## 
##                                   coef exp(coef) se(coef)      z       p
## FOIstandardized                -0.3455    0.7079   0.3285 -1.052 0.29297
## standardized_risk_score         0.3851    1.4697   0.3798  1.014 0.31063
## Trt                            -1.3295    0.2646   0.4678 -2.842 0.00449
## Bpseudoneutid50_D614G          -0.4862    0.6150   0.4908 -0.991 0.32187
## Day15pseudoneutid50_D614G       0.7199    2.0541   9.1491  0.079 0.93729
## I(Day15pseudoneutid50_D614G^2) -0.0983    0.9064   1.0962 -0.090 0.92855
## 
## Likelihood ratio test=12.1  on 6 df, p=0.05974
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G * Day15pseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G * 
##     Day15pseudoneutid50_D614G), data = dat.1)
## 
##                                                    coef exp(coef) se(coef)
## FOIstandardized                                 -0.3629    0.6956   0.3266
## standardized_risk_score                          0.3633    1.4380   0.3727
## Trt                                             -1.2999    0.2725   0.4475
## Bpseudoneutid50_D614G                            2.9004   18.1816   6.1345
## Day15pseudoneutid50_D614G                        2.4931   12.0987   4.7804
## Bpseudoneutid50_D614G:Day15pseudoneutid50_D614G -0.8016    0.4486   1.4502
##                                                      z       p
## FOIstandardized                                 -1.111 0.26650
## standardized_risk_score                          0.975 0.32977
## Trt                                             -2.905 0.00368
## Bpseudoneutid50_D614G                            0.473 0.63635
## Day15pseudoneutid50_D614G                        0.522 0.60200
## Bpseudoneutid50_D614G:Day15pseudoneutid50_D614G -0.553 0.58043
## 
## Likelihood ratio test=12.44  on 6 df, p=0.05286
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G + Day15pseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G + 
##     Day15pseudoneutid50_D614G), data = dat.1)
## 
##                               coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.34752   0.70644  0.32782 -1.060 0.28910
## standardized_risk_score    0.39723   1.48770  0.35421  1.121 0.26210
## Trt                       -1.34393   0.26082  0.44034 -3.052 0.00227
## Bpseudoneutid50_D614G     -0.48573   0.61525  0.49278 -0.986 0.32428
## Day15pseudoneutid50_D614G -0.09788   0.90675  0.68958 -0.142 0.88712
## 
## Likelihood ratio test=12.09  on 5 df, p=0.03353
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G), 
##     data = dat.1)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.3433    0.7094   0.3265 -1.051 0.29307
## standardized_risk_score  0.4042    1.4981   0.3542  1.141 0.25378
## Trt                     -1.3536    0.2583   0.4357 -3.106 0.00189
## Bpseudoneutid50_D614G   -0.5220    0.5934   0.4159 -1.255 0.20949
## 
## Likelihood ratio test=12.07  on 4 df, p=0.01682
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Day15pseudoneutid50_D614G), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_D614G), 
##     data = dat.1)
## 
##                              coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.3568    0.6999   0.3320 -1.075 0.28252
## standardized_risk_score    0.3775    1.4586   0.3485  1.083 0.27878
## Trt                       -1.3000    0.2725   0.4364 -2.979 0.00289
## Day15pseudoneutid50_D614G -0.4664    0.6273   0.5907 -0.789 0.42983
## 
## Likelihood ratio test=11.21  on 4 df, p=0.02432
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + Day15pseudoneutid50_BA.4.BA.5 + I(Day15pseudoneutid50_BA.4.BA.5^2)), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + 
##     Day15pseudoneutid50_BA.4.BA.5 + I(Day15pseudoneutid50_BA.4.BA.5^2)), 
##     data = dat.1)
## 
##                                        coef exp(coef) se(coef)      z       p
## FOIstandardized                    -0.39082   0.67650  0.33397 -1.170 0.24192
## standardized_risk_score             0.44598   1.56201  0.35217  1.266 0.20538
## Trt                                -1.32656   0.26539  0.48196 -2.752 0.00592
## Bpseudoneutid50_BA.4.BA.5          -0.63623   0.52928  0.44876 -1.418 0.15626
## Day15pseudoneutid50_BA.4.BA.5      -0.46895   0.62566  2.24326 -0.209 0.83441
## I(Day15pseudoneutid50_BA.4.BA.5^2)  0.03931   1.04009  0.41458  0.095 0.92446
## 
## Likelihood ratio test=15.12  on 6 df, p=0.01931
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 * Day15pseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 * 
##     Day15pseudoneutid50_BA.4.BA.5), data = dat.1)
## 
##                                                            coef exp(coef)
## FOIstandardized                                         -0.3963    0.6728
## standardized_risk_score                                  0.4624    1.5879
## Trt                                                     -1.3413    0.2615
## Bpseudoneutid50_BA.4.BA.5                               -1.5970    0.2025
## Day15pseudoneutid50_BA.4.BA.5                           -0.7192    0.4871
## Bpseudoneutid50_BA.4.BA.5:Day15pseudoneutid50_BA.4.BA.5  0.3065    1.3587
##                                                         se(coef)      z       p
## FOIstandardized                                           0.3337 -1.188 0.23499
## standardized_risk_score                                   0.3541  1.306 0.19161
## Trt                                                       0.4739 -2.830 0.00465
## Bpseudoneutid50_BA.4.BA.5                                 2.8898 -0.553 0.58053
## Day15pseudoneutid50_BA.4.BA.5                             1.4386 -0.500 0.61712
## Bpseudoneutid50_BA.4.BA.5:Day15pseudoneutid50_BA.4.BA.5   0.9028  0.340 0.73419
## 
## Likelihood ratio test=15.23  on 6 df, p=0.01856
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + Day15pseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + 
##     Day15pseudoneutid50_BA.4.BA.5), data = dat.1)
## 
##                                  coef exp(coef) se(coef)      z      p
## FOIstandardized               -0.3932    0.6749   0.3327 -1.182 0.2373
## standardized_risk_score        0.4418    1.5555   0.3494  1.264 0.2061
## Trt                           -1.3153    0.2684   0.4664 -2.820 0.0048
## Bpseudoneutid50_BA.4.BA.5     -0.6318    0.5316   0.4472 -1.413 0.1577
## Day15pseudoneutid50_BA.4.BA.5 -0.2616    0.7698   0.5056 -0.517 0.6049
## 
## Likelihood ratio test=15.12  on 5 df, p=0.009877
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                              coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.3707    0.6903   0.3275 -1.132 0.25778
## standardized_risk_score    0.4619    1.5871   0.3584  1.289 0.19754
## Trt                       -1.4067    0.2449   0.4402 -3.196 0.00139
## Bpseudoneutid50_BA.4.BA.5 -0.7528    0.4711   0.3771 -1.996 0.04593
## 
## Likelihood ratio test=14.85  on 4 df, p=0.005012
## n= 98, number of events= 23
coxph(update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), dat.1)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1)
## 
##                                  coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.3846    0.6807   0.3365 -1.143 0.25298
## standardized_risk_score        0.3880    1.4741   0.3346  1.160 0.24613
## Trt                           -1.1710    0.3101   0.4380 -2.673 0.00751
## Day15pseudoneutid50_BA.4.BA.5 -0.6690    0.5122   0.4026 -1.661 0.09662
## 
## Likelihood ratio test=13.1  on 4 df, p=0.01078
## n= 98, number of events= 23

Moderna

No treatment effect in either naive or non-naive.

coxph(update(f, ~. + naive + Trt), dat.ocp.moderna)
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = dat.ocp.moderna)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.1298    0.8782   0.1923 -0.675 0.49956
## standardized_risk_score  0.2056    1.2283   0.1441  1.427 0.15360
## naive                    1.0871    2.9657   0.3741  2.906 0.00367
## Trt                     -0.1180    0.8887   0.2388 -0.494 0.62124
## 
## Likelihood ratio test=13.62  on 4 df, p=0.008612
## n= 284, number of events= 78
coxph(update(f, ~. + naive + Trt), subset(dat.ocp.moderna, naive==0))
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = subset(dat.ocp.moderna, 
##     naive == 0))
## 
##                            coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.4871    0.6144   0.5445 -0.895 0.3710
## standardized_risk_score -0.4855    0.6154   0.2100 -2.312 0.0208
## naive                        NA        NA   0.0000     NA     NA
## Trt                     -0.5147    0.5977   0.7306 -0.705 0.4811
## 
## Likelihood ratio test=6.87  on 3 df, p=0.07628
## n= 64, number of events= 8
coxph(update(f, ~. + naive + Trt), subset(dat.ocp.moderna, naive==1))
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = subset(dat.ocp.moderna, 
##     naive == 1))
## 
##                             coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.03082   0.96965  0.20833 -0.148 0.8824
## standardized_risk_score  0.45535   1.57672  0.16296  2.794 0.0052
## naive                         NA        NA  0.00000     NA     NA
## Trt                     -0.07904   0.92400  0.25598 -0.309 0.7575
## 
## Likelihood ratio test=8.48  on 3 df, p=0.03705
## n= 220, number of events= 70

Distribution of D15 BA4BA5-specific ID50 is different between P and OC

par(mfrow=c(1,2))
myboxplot(Bpseudoneutid50_BA.4.BA.5~Trt, dat.1.moderna, test="w")
myboxplot(Day15pseudoneutid50_BA.4.BA.5~Trt, dat.1.moderna, test="w")

Among naive, there is significant interaction between Trt and D1 BA4BA5 ID50

coxph(update(f, ~. + Trt * Bpseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt * Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                                   coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.10876   0.89694  0.21194 -0.513 0.60782
## standardized_risk_score        0.51757   1.67794  0.17018  3.041 0.00236
## Trt                            1.43400   4.19546  0.80039  1.792 0.07319
## Bpseudoneutid50_BA.4.BA.5     -0.03369   0.96687  0.31280 -0.108 0.91422
## Trt:Bpseudoneutid50_BA.4.BA.5 -0.78765   0.45491  0.38980 -2.021 0.04332
## 
## Likelihood ratio test=22.09  on 5 df, p=0.0005028
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                               coef exp(coef) se(coef)      z      p
## FOIstandardized           -0.08466   0.91883  0.21020 -0.403 0.6871
## standardized_risk_score    0.52343   1.68781  0.16853  3.106 0.0019
## Trt                       -0.05426   0.94719  0.25656 -0.211 0.8325
## Bpseudoneutid50_BA.4.BA.5 -0.55763   0.57256  0.18591 -3.000 0.0027
## 
## Likelihood ratio test=18.02  on 4 df, p=0.001224
## n= 220, number of events= 70
coxph(update(f, ~. + Trt * Day15pseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt * Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                                        coef exp(coef)  se(coef)      z       p
## FOIstandardized                   -0.063658  0.938326  0.208384 -0.305 0.76000
## standardized_risk_score            0.419372  1.521006  0.158592  2.644 0.00818
## Trt                                2.167095  8.732879  1.238928  1.749 0.08026
## Day15pseudoneutid50_BA.4.BA.5     -0.006817  0.993206  0.346598 -0.020 0.98431
## Trt:Day15pseudoneutid50_BA.4.BA.5 -0.725744  0.483964  0.409206 -1.774 0.07614
## 
## Likelihood ratio test=18.29  on 5 df, p=0.002603
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                                   coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.04024   0.96056  0.20792 -0.194 0.84655
## standardized_risk_score        0.44264   1.55682  0.15841  2.794 0.00520
## Trt                            0.05208   1.05347  0.26166  0.199 0.84222
## Day15pseudoneutid50_BA.4.BA.5 -0.49862   0.60737  0.18590 -2.682 0.00731
## 
## Likelihood ratio test=15.02  on 4 df, p=0.004658
## n= 220, number of events= 70
coxph(update(f, ~. + Trt * Bpseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt * Bpseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                               coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.01409   0.98600  0.21342 -0.066 0.94734
## standardized_risk_score    0.48600   1.62579  0.16721  2.906 0.00366
## Trt                        1.57583   4.83477  1.56471  1.007 0.31388
## Bpseudoneutid50_D614G     -0.22904   0.79530  0.40054 -0.572 0.56745
## Trt:Bpseudoneutid50_D614G -0.48992   0.61268  0.46328 -1.058 0.29028
## 
## Likelihood ratio test=17.22  on 5 df, p=0.004097
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                              coef exp(coef)  se(coef)      z       p
## FOIstandardized          0.005631  1.005647  0.211626  0.027 0.97877
## standardized_risk_score  0.489978  1.632280  0.166749  2.938 0.00330
## Trt                     -0.042098  0.958776  0.256407 -0.164 0.86959
## Bpseudoneutid50_D614G   -0.591856  0.553299  0.210497 -2.812 0.00493
## 
## Likelihood ratio test=16.12  on 4 df, p=0.002862
## n= 220, number of events= 70
coxph(update(f, ~. + Trt * Day15pseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt * Day15pseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                                   coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.04257   0.95833  0.21104 -0.202 0.84015
## standardized_risk_score        0.42967   1.53675  0.16333  2.631 0.00852
## Trt                            2.75942  15.79061  2.68283  1.029 0.30369
## Day15pseudoneutid50_D614G     -0.33609   0.71456  0.52728 -0.637 0.52386
## Trt:Day15pseudoneutid50_D614G -0.67350   0.50992  0.63901 -1.054 0.29190
## 
## Likelihood ratio test=16.55  on 5 df, p=0.005445
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Day15pseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                               coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.02905   0.97137  0.20991 -0.138 0.88992
## standardized_risk_score    0.43341   1.54250  0.16353  2.650 0.00804
## Trt                       -0.04242   0.95847  0.25644 -0.165 0.86862
## Day15pseudoneutid50_D614G -0.78976   0.45395  0.29689 -2.660 0.00781
## 
## Likelihood ratio test=15.42  on 4 df, p=0.003899
## n= 220, number of events= 70

Additional marker models

coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G + Day15pseudoneutid50_D614G + I(Day15pseudoneutid50_D614G^2)), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G + 
##     Day15pseudoneutid50_D614G + I(Day15pseudoneutid50_D614G^2)), 
##     data = dat.1.moderna)
## 
##                                      coef  exp(coef)   se(coef)      z      p
## FOIstandardized                -5.814e-03  9.942e-01  2.114e-01 -0.028 0.9781
## standardized_risk_score         4.733e-01  1.605e+00  1.694e-01  2.794 0.0052
## Trt                            -3.537e-02  9.653e-01  2.567e-01 -0.138 0.8904
## Bpseudoneutid50_D614G          -4.341e-01  6.478e-01  2.870e-01 -1.513 0.1304
## Day15pseudoneutid50_D614G       9.463e+00  1.287e+04  6.180e+00  1.531 0.1257
## I(Day15pseudoneutid50_D614G^2) -1.195e+00  3.028e-01  7.478e-01 -1.598 0.1101
## 
## Likelihood ratio test=20.2  on 6 df, p=0.00255
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G * Day15pseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G * 
##     Day15pseudoneutid50_D614G), data = dat.1.moderna)
## 
##                                                     coef exp(coef) se(coef)
## FOIstandardized                                 -0.02009   0.98011  0.21239
## standardized_risk_score                          0.47970   1.61559  0.16983
## Trt                                             -0.04103   0.95980  0.25641
## Bpseudoneutid50_D614G                            3.60636  36.83171  2.59976
## Day15pseudoneutid50_D614G                        2.52712  12.51740  1.94240
## Bpseudoneutid50_D614G:Day15pseudoneutid50_D614G -0.94366   0.38920  0.61038
##                                                      z       p
## FOIstandardized                                 -0.095 0.92463
## standardized_risk_score                          2.825 0.00473
## Trt                                             -0.160 0.87285
## Bpseudoneutid50_D614G                            1.387 0.16538
## Day15pseudoneutid50_D614G                        1.301 0.19325
## Bpseudoneutid50_D614G:Day15pseudoneutid50_D614G -1.546 0.12210
## 
## Likelihood ratio test=19.83  on 6 df, p=0.002965
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G + Day15pseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G + 
##     Day15pseudoneutid50_D614G), data = dat.1.moderna)
## 
##                                coef exp(coef)  se(coef)      z      p
## FOIstandardized           -0.007339  0.992688  0.211648 -0.035 0.9723
## standardized_risk_score    0.462311  1.587738  0.167240  2.764 0.0057
## Trt                       -0.031277  0.969207  0.256769 -0.122 0.9030
## Bpseudoneutid50_D614G     -0.395893  0.673078  0.293522 -1.349 0.1774
## Day15pseudoneutid50_D614G -0.406311  0.666103  0.404493 -1.004 0.3151
## 
## Likelihood ratio test=17.16  on 5 df, p=0.004213
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                              coef exp(coef)  se(coef)      z       p
## FOIstandardized          0.005631  1.005647  0.211626  0.027 0.97877
## standardized_risk_score  0.489978  1.632280  0.166749  2.938 0.00330
## Trt                     -0.042098  0.958776  0.256407 -0.164 0.86959
## Bpseudoneutid50_D614G   -0.591856  0.553299  0.210497 -2.812 0.00493
## 
## Likelihood ratio test=16.12  on 4 df, p=0.002862
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Day15pseudoneutid50_D614G), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_D614G), 
##     data = dat.1.moderna)
## 
##                               coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.02905   0.97137  0.20991 -0.138 0.88992
## standardized_risk_score    0.43341   1.54250  0.16353  2.650 0.00804
## Trt                       -0.04242   0.95847  0.25644 -0.165 0.86862
## Day15pseudoneutid50_D614G -0.78976   0.45395  0.29689 -2.660 0.00781
## 
## Likelihood ratio test=15.42  on 4 df, p=0.003899
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + Day15pseudoneutid50_BA.4.BA.5 + I(Day15pseudoneutid50_BA.4.BA.5^2)), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + 
##     Day15pseudoneutid50_BA.4.BA.5 + I(Day15pseudoneutid50_BA.4.BA.5^2)), 
##     data = dat.1.moderna)
## 
##                                         coef exp(coef)  se(coef)      z       p
## FOIstandardized                     -0.16507   0.84784   0.21337 -0.774 0.43916
## standardized_risk_score              0.45693   1.57922   0.16953  2.695 0.00703
## Trt                                  0.09869   1.10373   0.26505  0.372 0.70963
## Bpseudoneutid50_BA.4.BA.5           -0.18224   0.83340   0.24952 -0.730 0.46517
## Day15pseudoneutid50_BA.4.BA.5        4.87481 130.94983   1.87375  2.602 0.00928
## I(Day15pseudoneutid50_BA.4.BA.5^2)  -0.97889   0.37573   0.34700 -2.821 0.00479
## 
## Likelihood ratio test=29.29  on 6 df, p=5.372e-05
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 * Day15pseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 * 
##     Day15pseudoneutid50_BA.4.BA.5), data = dat.1.moderna)
## 
##                                                              coef exp(coef)
## FOIstandardized                                          -0.13156   0.87673
## standardized_risk_score                                   0.45336   1.57359
## Trt                                                       0.04978   1.05104
## Bpseudoneutid50_BA.4.BA.5                                 5.66331 288.10120
## Day15pseudoneutid50_BA.4.BA.5                             2.57487  13.12966
## Bpseudoneutid50_BA.4.BA.5:Day15pseudoneutid50_BA.4.BA.5  -1.87482   0.15338
##                                                          se(coef)      z
## FOIstandardized                                           0.21151 -0.622
## standardized_risk_score                                   0.16885  2.685
## Trt                                                       0.26683  0.187
## Bpseudoneutid50_BA.4.BA.5                                 1.70177  3.328
## Day15pseudoneutid50_BA.4.BA.5                             0.84488  3.048
## Bpseudoneutid50_BA.4.BA.5:Day15pseudoneutid50_BA.4.BA.5   0.53345 -3.515
##                                                                p
## FOIstandardized                                         0.533957
## standardized_risk_score                                 0.007252
## Trt                                                     0.851993
## Bpseudoneutid50_BA.4.BA.5                               0.000875
## Day15pseudoneutid50_BA.4.BA.5                           0.002307
## Bpseudoneutid50_BA.4.BA.5:Day15pseudoneutid50_BA.4.BA.5 0.000441
## 
## Likelihood ratio test=32.41  on 6 df, p=1.363e-05
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + Day15pseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5 + 
##     Day15pseudoneutid50_BA.4.BA.5), data = dat.1.moderna)
## 
##                                    coef exp(coef)  se(coef)      z       p
## FOIstandardized               -0.076829  0.926048  0.209936 -0.366 0.71439
## standardized_risk_score        0.501798  1.651689  0.167333  2.999 0.00271
## Trt                           -0.002618  0.997386  0.264350 -0.010 0.99210
## Bpseudoneutid50_BA.4.BA.5     -0.445376  0.640583  0.233371 -1.908 0.05633
## Day15pseudoneutid50_BA.4.BA.5 -0.201700  0.817340  0.246766 -0.817 0.41371
## 
## Likelihood ratio test=18.67  on 5 df, p=0.002214
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Bpseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                               coef exp(coef) se(coef)      z      p
## FOIstandardized           -0.08466   0.91883  0.21020 -0.403 0.6871
## standardized_risk_score    0.52343   1.68781  0.16853  3.106 0.0019
## Trt                       -0.05426   0.94719  0.25656 -0.211 0.8325
## Bpseudoneutid50_BA.4.BA.5 -0.55763   0.57256  0.18591 -3.000 0.0027
## 
## Likelihood ratio test=18.02  on 4 df, p=0.001224
## n= 220, number of events= 70
coxph(update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), dat.1.moderna)
## Call:
## coxph(formula = update(f, ~. + Trt + Day15pseudoneutid50_BA.4.BA.5), 
##     data = dat.1.moderna)
## 
##                                   coef exp(coef) se(coef)      z       p
## FOIstandardized               -0.04024   0.96056  0.20792 -0.194 0.84655
## standardized_risk_score        0.44264   1.55682  0.15841  2.794 0.00520
## Trt                            0.05208   1.05347  0.26166  0.199 0.84222
## Day15pseudoneutid50_BA.4.BA.5 -0.49862   0.60737  0.18590 -2.682 0.00731
## 
## Likelihood ratio test=15.02  on 4 df, p=0.004658
## n= 220, number of events= 70
coxph(update(f, ~.  + Day15pseudoneutid50_BA.4.BA.5), subset(dat.1.moderna, Trt==1))
## Call:
## coxph(formula = update(f, ~. + Day15pseudoneutid50_BA.4.BA.5), 
##     data = subset(dat.1.moderna, Trt == 1))
## 
##                                  coef exp(coef) se(coef)      z        p
## FOIstandardized               -0.1627    0.8498   0.2699 -0.603 0.546488
## standardized_risk_score        0.4981    1.6456   0.1865  2.670 0.007581
## Day15pseudoneutid50_BA.4.BA.5 -0.7579    0.4686   0.2176 -3.484 0.000495
## 
## Likelihood ratio test=19.88  on 3 df, p=0.0001794
## n= 145, number of events= 47
coxph(update(f, ~.  + Day15pseudoneutid50_D614G), subset(dat.1.moderna, Trt==1))
## Call:
## coxph(formula = update(f, ~. + Day15pseudoneutid50_D614G), data = subset(dat.1.moderna, 
##     Trt == 1))
## 
##                              coef exp(coef) se(coef)      z       p
## FOIstandardized           -0.1406    0.8688   0.2749 -0.512 0.60893
## standardized_risk_score    0.5205    1.6829   0.1945  2.676 0.00745
## Day15pseudoneutid50_D614G -1.0358    0.3549   0.3641 -2.845 0.00444
## 
## Likelihood ratio test=17.49  on 3 df, p=0.000561
## n= 145, number of events= 47

Putting Pfizer and Moderna side by side

Omicron-specific antibodies are similar at D1, rise at D15, and more so when vaccines contain Omicron strains.

par(mfrow=c(1,2))
myboxplot(Bpseudoneutid50_BA.4.BA.5~Trt+company, subset(dat.ocp, naive==1), cex.axis=.8)
myboxplot(Day15pseudoneutid50_BA.4.BA.5~Trt+company, subset(dat.ocp, naive==1), cex.axis=.8)

Ancestral antibodies are not quite similar at D1, rise at D15, but not more so when vaccines contain Omicron strains.

par(mfrow=c(1,2))
myboxplot(Bpseudoneutid50_D614G~Trt+company, subset(dat.ocp, naive==1), cex.axis=.8)
myboxplot(Day15pseudoneutid50_D614G~Trt+company, subset(dat.ocp, naive==1), cex.axis=.8)

fits=list()
fits[["Pfz,P"]] = coxph(update(f, ~.  + Day15pseudoneutid50_D614G), subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0))
fits[["Pfz,O"]] = coxph(update(f, ~.  + Day15pseudoneutid50_D614G), subset(dat.ocp, naive==1 & company=="Pfz" & Trt==1))
fits[["Mdn,P"]] = coxph(update(f, ~.  + Day15pseudoneutid50_D614G), subset(dat.ocp, naive==1 & company=="Mdn" & Trt==0))
fits[["Mdn,O"]] = coxph(update(f, ~.  + Day15pseudoneutid50_D614G), subset(dat.ocp, naive==1 & company=="Mdn" & Trt==1))
tab = getFormattedSummary(fits, robust=F, type=5)
tab
##                           Pfz,P   Pfz,O   Mdn,P   Mdn,O    
## FOIstandardized           "-0.49" "-0.22" "0.19"  "-0.14"  
## standardized_risk_score   "0.36"  "0.36"  "0.15"  "0.52**" 
## Day15pseudoneutid50_D614G "-0.15" "-0.70" "-0.37" "-1.04**"

Are risk scores distribution different?

myboxplot(standardized_risk_score    ~Trt+company, subset(dat.ocp, naive==1), cex.axis=.8)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score*Trt, subset(dat.ocp, naive==1 & company=="Mdn"))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score * Trt, data = subset(dat.ocp, naive == 
##     1 & company == "Mdn"))
## 
##                                coef exp(coef) se(coef)      z     p
## standardized_risk_score      0.1836    1.2015   0.2949  0.623 0.534
## Trt                         -0.2121    0.8089   0.2839 -0.747 0.455
## standardized_risk_score:Trt  0.3793    1.4613   0.3523  1.077 0.282
## 
## Likelihood ratio test=9.58  on 3 df, p=0.02251
## n= 220, number of events= 70

BA4BA5 marker. Three out of the four effect sizes are comparable to each other, but in the Moderna prototype arm there is no association between BA4BA5 marker and risk. This is quite intriguing - if we view each column above as a correlates analysis, we have three positive results and one negative result.

fits=list()
fits[["Pfz,P"]] = coxph(update(f, ~.  + Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0))
fits[["Pfz,O"]] = coxph(update(f, ~.  + Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp, naive==1 & company=="Pfz" & Trt==1))
fits[["Mdn,P"]] = coxph(update(f, ~.  + Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp, naive==1 & company=="Mdn" & Trt==0))
fits[["Mdn,O"]] = coxph(update(f, ~.  + Day15pseudoneutid50_BA.4.BA.5), subset(dat.ocp, naive==1 & company=="Mdn" & Trt==1))
tab = getFormattedSummary(fits, robust=F, type=5)
tab
##                               Pfz,P   Pfz,O   Mdn,P  Mdn,O    
## FOIstandardized               "-0.51" "-0.29" "0.17" "-0.16"  
## standardized_risk_score       "0.25"  "0.44"  "0.16" "0.50**" 
## Day15pseudoneutid50_BA.4.BA.5 "-0.62" "-0.75" "0.00" "-0.76**"

Correlation between ancestral and BA4BA5 ID50s in Pfz,P and Pfz,O separately

par(mfrow=c(1,2))
lim=c(2.5,5.3)
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0), asp=1, xlim=lim, ylim=lim, main="Pfz, Prototype")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==1), asp=1, xlim=lim, ylim=lim, main="Pfz, Omicron")

Risk models

ID50 Score

dat$D1_id50=scale(dat$Bpseudoneutid50_MDW,scale=F)
dat$Day15_id50=scale(dat$Day15pseudoneutid50_MDW,scale=F)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ FOIstandardized + standardized_risk_score + naive + Day15_id50, dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     FOIstandardized + standardized_risk_score + naive + Day15_id50, 
##     data = dat)
## 
##                              coef exp(coef)  se(coef)      z        p
## FOIstandardized          0.001851  1.001853  0.082550  0.022  0.98211
## standardized_risk_score  0.220804  1.247079  0.084345  2.618  0.00885
## naive                    1.054369  2.870165  0.210874  5.000 5.73e-07
## Day15_id50              -0.371085  0.689986  0.134860 -2.752  0.00593
## 
## Likelihood ratio test=77.26  on 4 df, p=6.61e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + D1_id50 + Day15_id50 + I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = dat)
## 
##                             coef exp(coef) se(coef)      z        p
## standardized_risk_score  0.24172   1.27343  0.08176  2.956 0.003112
## naive                    0.66527   1.94501  0.22308  2.982 0.002862
## D1_id50                 -0.44490   0.64089  0.16269 -2.735 0.006245
## Day15_id50              -0.49043   0.61236  0.25055 -1.957 0.050294
## I(Day15_id50^2)         -0.98915   0.37189  0.27479 -3.600 0.000319
## 
## Likelihood ratio test=103.4  on 5 df, p=< 2.2e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + naive*(D1_id50 + Day15_id50 + I(Day15_id50^2)), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + naive * (D1_id50 + Day15_id50 + 
##         I(Day15_id50^2)), data = dat)
## 
##                             coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.23644   1.26673  0.08174  2.892 0.00382
## naive                    0.56240   1.75488  0.22961  2.449 0.01431
## D1_id50                 -0.91307   0.40129  0.36906 -2.474 0.01336
## Day15_id50              -0.76230   0.46659  0.56949 -1.339 0.18071
## I(Day15_id50^2)         -0.75581   0.46963  0.46669 -1.620 0.10534
## naive:D1_id50            0.56603   1.76126  0.40890  1.384 0.16628
## naive:Day15_id50         0.33588   1.39917  0.63396  0.530 0.59624
## naive:I(Day15_id50^2)   -0.13493   0.87377  0.55767 -0.242 0.80881
## 
## Likelihood ratio test=108  on 8 df, p=< 2.2e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + naive*D1_id50 + Day15_id50 + I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + naive * D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = dat)
## 
##                             coef exp(coef) se(coef)      z        p
## standardized_risk_score  0.23504   1.26496  0.08166  2.878 0.003998
## naive                    0.53717   1.71115  0.21176  2.537 0.011192
## D1_id50                 -1.02753   0.35789  0.30465 -3.373 0.000744
## Day15_id50              -0.47621   0.62113  0.24694 -1.928 0.053804
## I(Day15_id50^2)         -0.88168   0.41409  0.26717 -3.300 0.000966
## naive:D1_id50            0.70604   2.02595  0.32593  2.166 0.030292
## 
## Likelihood ratio test=107.7  on 6 df, p=< 2.2e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + D1_id50 + naive*Day15_id50 + naive*I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + D1_id50 + naive * Day15_id50 + 
##         naive * I(Day15_id50^2), data = dat)
## 
##                             coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.24273   1.27472  0.08174  2.969 0.00298
## naive                    0.63995   1.89639  0.23269  2.750 0.00596
## D1_id50                 -0.44191   0.64281  0.16069 -2.750 0.00596
## Day15_id50              -1.19176   0.30368  0.48297 -2.468 0.01360
## I(Day15_id50^2)         -0.75693   0.46911  0.45572 -1.661 0.09673
## naive:Day15_id50         0.84626   2.33092  0.51659  1.638 0.10139
## naive:I(Day15_id50^2)   -0.14280   0.86693  0.54910 -0.260 0.79482
## 
## Likelihood ratio test=106.2  on 7 df, p=< 2.2e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + D1_id50 + Day15_id50 + naive*I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + D1_id50 + Day15_id50 + 
##         naive * I(Day15_id50^2), data = dat)
## 
##                             coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.24081   1.27228  0.08177  2.945 0.00323
## naive                    0.70910   2.03216  0.24324  2.915 0.00355
## D1_id50                 -0.44461   0.64108  0.16272 -2.732 0.00629
## Day15_id50              -0.52303   0.59272  0.26075 -2.006 0.04487
## I(Day15_id50^2)         -0.70683   0.49321  0.62738 -1.127 0.25990
## naive:I(Day15_id50^2)   -0.34038   0.71150  0.71376 -0.477 0.63345
## 
## Likelihood ratio test=103.6  on 6 df, p=< 2.2e-16
## n= 985, number of events= 213
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + D1_id50 + naive*Day15_id50 + I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + D1_id50 + naive * Day15_id50 + 
##         I(Day15_id50^2), data = dat)
## 
##                             coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.24300   1.27507  0.08171  2.974 0.00294
## naive                    0.61857   1.85626  0.21646  2.858 0.00427
## D1_id50                 -0.44083   0.64350  0.16055 -2.746 0.00604
## Day15_id50              -1.21649   0.29627  0.48543 -2.506 0.01221
## I(Day15_id50^2)         -0.86024   0.42306  0.26191 -3.285 0.00102
## naive:Day15_id50         0.88834   2.43109  0.50261  1.767 0.07715
## 
## Likelihood ratio test=106.2  on 6 df, p=< 2.2e-16
## n= 985, number of events= 213

ID50 BA4BA5

dat$D1_id50=scale(dat$Bpseudoneutid50_BA.4.BA.5,scale=F)
dat$Day15_id50=scale(dat$Day15pseudoneutid50_BA.4.BA.5,scale=F)

coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + naive*D1_id50 + Day15_id50 + I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + naive * D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = dat)
## 
##                            coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.2190    1.2448   0.0811  2.700 0.00694
## naive                    0.4651    1.5921   0.2136  2.177 0.02946
## D1_id50                 -0.9630    0.3818   0.2799 -3.441 0.00058
## Day15_id50              -0.4177    0.6586   0.2126 -1.964 0.04948
## I(Day15_id50^2)         -0.4346    0.6475   0.1563 -2.779 0.00545
## naive:D1_id50            0.6896    1.9930   0.2910  2.370 0.01779
## 
## Likelihood ratio test=106.1  on 6 df, p=< 2.2e-16
## n= 985, number of events= 213
# filter out those with undetectable D1
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + naive + naive*D1_id50 + Day15_id50 + I(Day15_id50^2), subset(dat, D1_id50 > -1.06))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + naive + naive * D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = subset(dat, D1_id50 > -1.06))
## 
##                            coef exp(coef) se(coef)      z      p
## standardized_risk_score  0.0757    1.0786   0.1045  0.724 0.4688
## naive                    0.4559    1.5776   0.3107  1.467 0.1423
## D1_id50                 -0.9408    0.3903   0.4848 -1.941 0.0523
## Day15_id50              -0.6463    0.5240   0.2964 -2.180 0.0292
## I(Day15_id50^2)         -0.6404    0.5271   0.3936 -1.627 0.1037
## naive:D1_id50            0.8220    2.2751   0.5404  1.521 0.1282
## 
## Likelihood ratio test=63.51  on 6 df, p=8.688e-12
## n= 699, number of events= 117
# fit model to get inference for D1_id50 in the naive
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + I(1-naive)*D1_id50 + Day15_id50 + I(Day15_id50^2), dat)
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + I(1 - naive) * D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = dat)
## 
##                            coef exp(coef) se(coef)      z       p
## standardized_risk_score  0.2190    1.2448   0.0811  2.700 0.00694
## I(1 - naive)            -0.4651    0.6281   0.2136 -2.177 0.02946
## D1_id50                 -0.2733    0.7608   0.1396 -1.958 0.05027
## Day15_id50              -0.4177    0.6586   0.2126 -1.964 0.04948
## I(Day15_id50^2)         -0.4346    0.6475   0.1563 -2.779 0.00545
## I(1 - naive):D1_id50    -0.6896    0.5018   0.2910 -2.370 0.01779
## 
## Likelihood ratio test=106.1  on 6 df, p=< 2.2e-16
## n= 985, number of events= 213
# filter out those with undetectable D1
coxph(Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ standardized_risk_score + I(1-naive)*D1_id50 + Day15_id50 + I(Day15_id50^2), subset(dat, D1_id50 > -1.06))
## Call:
## coxph(formula = Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ 
##     standardized_risk_score + I(1 - naive) * D1_id50 + Day15_id50 + 
##         I(Day15_id50^2), data = subset(dat, D1_id50 > -1.06))
## 
##                            coef exp(coef) se(coef)      z      p
## standardized_risk_score  0.0757    1.0786   0.1045  0.724 0.4688
## I(1 - naive)            -0.4559    0.6339   0.3107 -1.467 0.1423
## D1_id50                 -0.1188    0.8880   0.3228 -0.368 0.7128
## Day15_id50              -0.6463    0.5240   0.2964 -2.180 0.0292
## I(Day15_id50^2)         -0.6404    0.5271   0.3936 -1.627 0.1037
## I(1 - naive):D1_id50    -0.8220    0.4395   0.5404 -1.521 0.1282
## 
## Likelihood ratio test=63.51  on 6 df, p=8.688e-12
## n= 699, number of events= 117

The effect of risk score is different between models with and without double naive (naive and with undetectable D1_id50).

dat$D1_id50=scale(dat$Bpseudoneutid50_BA.4.BA.5,scale=F)

myboxplot(standardized_risk_score~I(1-naive)*I(D1_id50 > -1.06), dat, ylab="standardized_risk_score", names=c("N, D1 undet", "NN, D1 undet", "N, D1 det", "NN, D1 det"))

fit=lm(standardized_risk_score ~ I(1-naive) * I(D1_id50 > -1.06), dat); summary(fit)
## 
## Call:
## lm(formula = standardized_risk_score ~ I(1 - naive) * I(D1_id50 > 
##     -1.06), data = dat)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.5176 -0.5421  0.1354  0.6626  2.0105 
## 
## Coefficients:
##                                     Estimate Std. Error t value Pr(>|t|)    
## (Intercept)                          0.03930    0.06026   0.652 0.514516    
## I(1 - naive)                         0.58424    0.29421   1.986 0.047336 *  
## I(D1_id50 > -1.06)TRUE               0.13356    0.08022   1.665 0.096237 .  
## I(1 - naive):I(D1_id50 > -1.06)TRUE -1.15269    0.30374  -3.795 0.000157 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.9976 on 981 degrees of freedom
## Multiple R-squared:  0.06359,    Adjusted R-squared:  0.06073 
## F-statistic: 22.21 on 3 and 981 DF,  p-value: 6.459e-14
fit=lm(standardized_risk_score ~ I(1-naive), subset(dat, D1_id50 <= -1.06)); summary(fit)
## 
## Call:
## lm(formula = standardized_risk_score ~ I(1 - naive), data = subset(dat, 
##     D1_id50 <= -1.06))
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -5.2614 -0.4698  0.1859  0.5916  1.9658 
## 
## Coefficients:
##              Estimate Std. Error t value Pr(>|t|)  
## (Intercept)    0.0393     0.0567   0.693   0.4888  
## I(1 - naive)   0.5842     0.2768   2.111   0.0357 *
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.9385 on 284 degrees of freedom
## Multiple R-squared:  0.01545,    Adjusted R-squared:  0.01198 
## F-statistic: 4.455 on 1 and 284 DF,  p-value: 0.03566
f=Surv(COVIDtimeD22toD181, COVIDIndD22toD181) ~ FOIstandardized + standardized_risk_score

dat.ocp2=subset(dat_proc, ph1.D15==1 & treatment_assigned %in% c(
    "Wildtype/Prototype (Pfizer 1)"
  , "Omicron (Pfizer 1)"
  , "Omicron + Wildtype/Prototype (Pfizer 1)"
  # , "Omicron BA.4/5 + Prototype (Pfizer 2)"
  # , "Omicron BA.1 + Prototype (Pfizer 2)"
  )
)
dat.ocp2$Trt=ifelse(dat.ocp2$treatment_assigned == "Wildtype/Prototype (Pfizer 1)", 0, 1)

coxph(update(f, ~. + naive + Trt), dat.ocp2)
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = dat.ocp2)
## 
##                            coef exp(coef) se(coef)      z       p
## FOIstandardized         -0.1126    0.8935   0.2984 -0.377 0.70591
## standardized_risk_score  0.2795    1.3224   0.2878  0.971 0.33154
## naive                    0.8310    2.2955   0.4551  1.826 0.06787
## Trt                     -1.1399    0.3199   0.3749 -3.040 0.00236
## 
## Likelihood ratio test=12.14  on 4 df, p=0.01631
## n= 151, number of events= 30
coxph(update(f, ~. + naive + Trt), subset(dat.ocp2, naive==0))
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = subset(dat.ocp2, 
##     naive == 0))
## 
##                             coef exp(coef) se(coef)      z     p
## FOIstandardized          0.59531   1.81359  0.61480  0.968 0.333
## standardized_risk_score  0.04664   1.04775  0.52826  0.088 0.930
## naive                         NA        NA  0.00000     NA    NA
## Trt                     -0.52997   0.58862  0.77255 -0.686 0.493
## 
## Likelihood ratio test=1.38  on 3 df, p=0.7098
## n= 53, number of events= 7
coxph(update(f, ~. + naive + Trt), subset(dat.ocp2, naive==1))
## Call:
## coxph(formula = update(f, ~. + naive + Trt), data = subset(dat.ocp2, 
##     naive == 1))
## 
##                            coef exp(coef) se(coef)      z      p
## FOIstandardized         -0.3243    0.7231   0.3318 -0.977 0.3285
## standardized_risk_score  0.4130    1.5113   0.3592  1.150 0.2503
## naive                        NA        NA   0.0000     NA     NA
## Trt                     -1.3346    0.2633   0.4359 -3.062 0.0022
## 
## Likelihood ratio test=10.59  on 3 df, p=0.01415
## n= 98, number of events= 23
dat.1=subset(dat.ocp2, naive==1)

B and D15 marker

table(dat$Bpseudoneutid50_MDWcat, dat$Day15pseudoneutid50_MDWcat)
##              
##               (-Inf,3.62] (3.62,4.07] (4.07, Inf]
##   (-Inf,2.56]         228          80          20
##   (2.56,3.27]          94         155          80
##   (3.27, Inf]           6          94         228
corplot(Day15pseudoneutid50_MDW~Bpseudoneutid50_MDW, dat, col=ifelse(dat$naive==1,1,2))

# fit demming regression
dat.n=subset(dat, naive==1)
dat.nn=subset(dat, naive==0)

fit.n =  Deming(dat.n$Bpseudoneutid50_MDW,  dat.n$Day15pseudoneutid50_MDW,  boot = TRUE)
fit.nn = Deming(dat.nn$Bpseudoneutid50_MDW, dat.nn$Day15pseudoneutid50_MDW, boot = TRUE)

summary(fit.n)
##                                           est    se(est)    (lower    upper)
## Intercept                           1.7871909 0.09110302 1.6060820 1.9576747
## Slope                               0.7210016 0.03387975 0.6587173 0.7917871
## sigma.dat.n$Bpseudoneutid50_MDW     0.2985262 0.01199177 0.2758940 0.3226616
## sigma.dat.n$Day15pseudoneutid50_MDW 0.2985262 0.01199177 0.2758940 0.3226616
##                                           p.value
## Intercept                            1.101506e-85
## Slope                               1.695729e-100
## sigma.dat.n$Bpseudoneutid50_MDW     8.584826e-137
## sigma.dat.n$Day15pseudoneutid50_MDW 8.584826e-137
summary(fit.nn)
##                                            est    se(est)    (lower    upper)
## Intercept                            1.5126849 0.23922704 1.0462625 1.9694045
## Slope                                0.7497295 0.06739409 0.6212233 0.8797335
## sigma.dat.nn$Bpseudoneutid50_MDW     0.2761024 0.01648200 0.2426575 0.3060327
## sigma.dat.nn$Day15pseudoneutid50_MDW 0.2761024 0.01648200 0.2426575 0.3060327
##                                           p.value
## Intercept                            2.561708e-10
## Slope                                9.527661e-29
## sigma.dat.nn$Bpseudoneutid50_MDW     5.497849e-63
## sigma.dat.nn$Day15pseudoneutid50_MDW 5.497849e-63
par(mfrow=c(2,1), mar=c(3,4,2,2))
lim=range(c(dat$Bpseudoneutid50_MDW, dat$Day15pseudoneutid50_MDW))
corplot(Day15pseudoneutid50_MDW~Bpseudoneutid50_MDW, dat.n, add.deming.fit = T, xlim=lim, ylim=lim, xlab="", main="Naive", method="pearson")
corplot(Day15pseudoneutid50_MDW~Bpseudoneutid50_MDW, dat.nn, add.deming.fit = T, xlim=lim, ylim=lim, main="Non-naive", method="pearson")
title(xlab="Bpseudoneutid50_MDW", line=2)

distribution

table(dat$Bpseudoneutid50_MDWcat, dat$Day15pseudoneutid50_MDWcat)
##              
##               (-Inf,3.62] (3.62,4.07] (4.07, Inf]
##   (-Inf,2.56]         228          80          20
##   (2.56,3.27]          94         155          80
##   (3.27, Inf]           6          94         228
table(dat$Bpseudoneutid50_MDWcat, dat$Day15pseudoneutid50_MDWcat, dat$naive)
## , ,  = 0
## 
##              
##               (-Inf,3.62] (3.62,4.07] (4.07, Inf]
##   (-Inf,2.56]          11           6           3
##   (2.56,3.27]          24          42          26
##   (3.27, Inf]           5          67         172
## 
## , ,  = 1
## 
##              
##               (-Inf,3.62] (3.62,4.07] (4.07, Inf]
##   (-Inf,2.56]         217          74          17
##   (2.56,3.27]          70         113          54
##   (3.27, Inf]           1          27          56
# all cases have covid lineage observed
mytable(dat_proc$COVIDlineageObserved, dat_proc$COVIDlineage)
##        
##         BA.2 BA.4 BA.5 XBB.1.5 XBB<ca>0.10  XZ <NA>
##   FALSE   23    0   83      13           0   0    0
##   TRUE    62   24  161      15           1   1    0
##   <NA>     0    0    0       0           0   0  857
mytable(dat_proc$COVIDlineageObserved, dat_proc$COVIDIndD22toend)
##        
##           0   1 <NA>
##   FALSE  36  83    0
##   TRUE   60 180   24
##   <NA>  857   0    0

save the risk score from covail_data_processed_20240205.csv as a separate file that will be treated as the source of risk score

dat1=read.csv("/trials/covpn/COVAILcorrelates/analysis/correlates/adata/covail_data_processed_20240205.csv")
write.csv(subset(dat1, select=c(Ptid, risk_score, standardized_risk_score)), row.names=F, file="/trials/covpn/COVAILcorrelates/analysis/correlates/adata/risk_score.csv")

There is a difference in risk score between 0205 and 0206 analysis ready datasets

dat1=read.csv("/trials/covpn/COVAILcorrelates/analysis/mapping_immune_correlates/adata/covail_mapped_data_20240205.csv")
dat2=read.csv("/trials/covpn/COVAILcorrelates/analysis/mapping_immune_correlates/adata/covail_mapped_data_20240206.csv")
nrow(dat1)
nrow(dat2)

cbind(dat1$COVIDIndD22toD181, dat2$COVIDIndD22toD181)[1:100,]


dat1=read.csv("/trials/covpn/COVAILcorrelates/analysis/correlates/adata/covail_data_processed_20240205.csv")
dat2=read.csv("/trials/covpn/COVAILcorrelates/analysis/correlates/adata/covail_data_processed_20240206.csv")
dat3=read.csv("/trials/covpn/COVAILcorrelates/analysis/correlates/adata/covail_data_processed_20240211.csv")
nrow(dat1)
nrow(dat2)
nrow(dat3)

with(subset(dat1,ph1.D15==1), fastauc(risk_score, COVIDIndD22toD181))
with(subset(dat2,ph1.D15==1), fastauc(risk_score, COVIDIndD22toD181))


dat1=read.csv("/trials/covpn/COVAILcorrelates/analysis/mapping_immune_correlates/adata/covail_mapped_data_20240208.csv")
dat2=read.csv("/trials/covpn/COVAILcorrelates/analysis/mapping_immune_correlates/adata/covail_mapped_data_20240211.csv")

rbind(dat1[16,-182],dat2[16,]) # COVIDtimeD22toend

setdiff(names(dat1), names(dat2))

mytable(dat2$COVIDIndD92toD181, dat2$COVIDtimeD92toD181)

sanofi markers

with(dat_mapped, table(treatment_actual %in% c("Beta (Sanofi)", "Beta + Prototype (Sanofi)", "Prototype (Sanofi)"), TrtSanofi))
##        TrtSanofi
##            0    1
##   FALSE 1110    0
##   TRUE     0  152
summary(dat.sanofi[,c("Day29"%.%assays[1:5])])
##  Day29pseudoneutid50_D614G Day29pseudoneutid50_Delta Day29pseudoneutid50_Beta
##  Min.   :2.964             Min.   :2.761             Min.   :2.450           
##  1st Qu.:3.747             1st Qu.:3.542             1st Qu.:3.413           
##  Median :4.127             Median :3.846             Median :3.813           
##  Mean   :4.118             Mean   :3.892             Mean   :3.821           
##  3rd Qu.:4.457             3rd Qu.:4.260             3rd Qu.:4.238           
##  Max.   :5.195             Max.   :5.036             Max.   :5.136           
##  NA's   :6                 NA's   :6                 NA's   :6               
##  Day29pseudoneutid50_BA.1 Day29pseudoneutid50_BA.4.BA.5
##  Min.   :1.301            Min.   :1.301                
##  1st Qu.:2.769            1st Qu.:2.693                
##  Median :3.322            Median :3.155                
##  Mean   :3.226            Mean   :3.091                
##  3rd Qu.:3.720            3rd Qu.:3.543                
##  Max.   :4.865            Max.   :4.507                
##  NA's   :6                NA's   :6
summary(dat.sanofi[,c("Day15"%.%assays[1:5])])
##  Day15pseudoneutid50_D614G Day15pseudoneutid50_Delta Day15pseudoneutid50_Beta
##  Min.   :2.830             Min.   :2.537             Min.   :2.290           
##  1st Qu.:3.657             1st Qu.:3.325             1st Qu.:3.257           
##  Median :3.922             Median :3.612             Median :3.611           
##  Mean   :3.971             Mean   :3.657             Mean   :3.633           
##  3rd Qu.:4.278             3rd Qu.:3.982             3rd Qu.:4.028           
##  Max.   :4.929             Max.   :4.733             Max.   :4.913           
##  NA's   :6                 NA's   :6                 NA's   :6               
##  Day15pseudoneutid50_BA.1 Day15pseudoneutid50_BA.4.BA.5
##  Min.   :1.301            Min.   :1.301                
##  1st Qu.:2.732            1st Qu.:2.618                
##  Median :3.191            Median :3.021                
##  Mean   :3.204            Mean   :3.002                
##  3rd Qu.:3.612            3rd Qu.:3.489                
##  Max.   :4.612            Max.   :4.493                
##  NA's   :6                NA's   :6
with(subset(dat_mapped, TrtSanofi==1), mytable(naive, COVIDIndD36toD181))
##      COVIDIndD36toD181
## naive  0  1 <NA>
##     0 56  4    2
##     1 66 13   11
with(subset(dat_mapped, TrtSanofi==1), mytable(naive, COVIDIndD22toD181))
##      COVIDIndD22toD181
## naive  0  1 <NA>
##     0 56  4    2
##     1 65 18    7

Correlation is high between BA4BA5 ID50 and ancestral ID50 in both naive and nnaive (higher in the latter)

par(mfrow=c(1,2))
lim=c(2.5,5.3)
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==1), asp=1, xlim=lim, ylim=lim, main="COVAIL Sanofi Naive")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, dat.sanofi, asp=1, xlim=lim, ylim=lim, main="COVAIL Sanofi")

# corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==0), asp=1, xlim=lim, ylim=lim)

Comparing with Pfz,P in the naive

par(mfrow=c(2,2))
lim=c(1.2,5.5)
myboxplot(list(subset(dat.sanofi, naive==1, Day15pseudoneutid50_D614G, drop=T),
               subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0,Day15pseudoneutid50_D614G, drop=T)), test="w", main="D15 Ancestral ID50", ylim=lim, names=c("Sanofi, naive", "Pfz,P, naive"), ylab="")
myboxplot(list(subset(dat.sanofi, naive==1, Day15pseudoneutid50_BA.4.BA.5, drop=T),
               subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0,Day15pseudoneutid50_BA.4.BA.5, drop=T)), test="w", main="D15 BA4BA5 ID50", ylim=lim, names=c("Sanofi, naive", "Pfz,P, naive"), ylab="")

corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==1), asp=1, xlim=lim, ylim=lim, main="Sanofi Naive")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0, c(Day15pseudoneutid50_D614G, Day15pseudoneutid50_BA.4.BA.5)), asp=1, xlim=lim, ylim=lim, main="Pfz,P Naive")

Comparing with Pfz,P in the naive, separately by Sanofi,P and Sanofi,NP

par(mfrow=c(1,3))
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)"), asp=1, xlim=lim, ylim=lim, main="Sanofi,P Naive")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)"), asp=1, xlim=lim, ylim=lim, main="Sanofi,NP Naive")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0, c(Day15pseudoneutid50_D614G, Day15pseudoneutid50_BA.4.BA.5)), asp=1, xlim=lim, ylim=lim, main="Pfz,P Naive")

Comparing with Pfz,P in the non-naive

par(mfrow=c(2,2))
lim=c(1.2,5.5)
myboxplot(list(subset(dat.sanofi, naive==0, Day15pseudoneutid50_D614G, drop=T),
               subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0,Day15pseudoneutid50_D614G, drop=T)), test="w", main="D15 Ancestral ID50", ylim=lim, names=c("Sanofi, Non-naive", "Pfz,P, Non-naive"), ylab="")
myboxplot(list(subset(dat.sanofi, naive==0, Day15pseudoneutid50_BA.4.BA.5, drop=T),
               subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0,Day15pseudoneutid50_BA.4.BA.5, drop=T)), test="w", main="D15 BA4BA5 ID50", ylim=lim, names=c("Sanofi, Non-naive", "Pfz,P, Non-naive"), ylab="")

corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.sanofi, naive==0), asp=1, xlim=lim, ylim=lim, main="Sanofi Non-naive")
corplot(Day15pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_D614G, subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0, c(Day15pseudoneutid50_D614G, Day15pseudoneutid50_BA.4.BA.5)), asp=1, xlim=lim, ylim=lim, main="Pfz,P Non-naive")

Baseline correlation, in the naive

par(mfrow=c(2,2))
lim=c(1.2,5.5)
myboxplot(list(subset(dat.sanofi, naive==1, Bpseudoneutid50_D614G, drop=T),
               subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0,Bpseudoneutid50_D614G, drop=T)), test="w", main="D1 Ancestral ID50", ylim=lim, names=c("Sanofi, naive", "Pfz,P, naive"), ylab="")
myboxplot(list(subset(dat.sanofi, naive==1, Bpseudoneutid50_BA.4.BA.5, drop=T),
               subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0,Bpseudoneutid50_BA.4.BA.5, drop=T)), test="w", main="D1 BA4BA5 ID50", ylim=lim, names=c("Sanofi, naive", "Pfz,P, naive"), ylab="")

corplot(Bpseudoneutid50_BA.4.BA.5~Bpseudoneutid50_D614G, subset(dat.sanofi, naive==1), asp=1, xlim=lim, ylim=lim, main="Sanofi Naive")
corplot(Bpseudoneutid50_BA.4.BA.5~Bpseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0, c(Bpseudoneutid50_D614G, Bpseudoneutid50_BA.4.BA.5)), asp=1, xlim=lim, ylim=lim, main="Pfz,P Naive")

Baseline correlation, in the non-naive

par(mfrow=c(2,2))
lim=c(1.2,5.5)
myboxplot(list(subset(dat.sanofi, naive==0, Bpseudoneutid50_D614G, drop=T),
               subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0,Bpseudoneutid50_D614G, drop=T)), test="w", main="D1 Ancestral ID50", ylim=lim, names=c("Sanofi, Non-naive", "Pfz,P, Non-naive"), ylab="")
myboxplot(list(subset(dat.sanofi, naive==0, Bpseudoneutid50_BA.4.BA.5, drop=T),
               subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0,Bpseudoneutid50_BA.4.BA.5, drop=T)), test="w", main="D1 BA4BA5 ID50", ylim=lim, names=c("Sanofi, Non-naive", "Pfz,P, Non-naive"), ylab="")

corplot(Bpseudoneutid50_BA.4.BA.5~Bpseudoneutid50_D614G, subset(dat.sanofi, naive==0), asp=1, xlim=lim, ylim=lim, main="Sanofi Non-naive")
corplot(Bpseudoneutid50_BA.4.BA.5~Bpseudoneutid50_D614G, subset(dat.ocp, naive==0 & company=="Pfz" & Trt==0, c(Bpseudoneutid50_D614G, Bpseudoneutid50_BA.4.BA.5)), asp=1, xlim=lim, ylim=lim, main="Pfz,P Non-naive")

Interaction plot, naive

par(mfrow=c(1,2))
lim=c(1.2,4.8)
# myboxplot(subset(dat.sanofi, naive==1, c(Day15pseudoneutid50_D614G, Day15pseudoneutid50_BA.4.BA.5)), names=c("ancestral", "BA4BA5"), main="Sanofi, naive", add.interaction=T)
# myboxplot(subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0, c(Day15pseudoneutid50_D614G, Day15pseudoneutid50_BA.4.BA.5)), names=c("ancestral", "BA4BA5"), main="Pfz,P, naive", add.interaction=T)

Correlation of fold change between ancestral and BA4BA5

dat.sanofi$Day15overBpseudoneutid50_BA.4.BA.5 = dat.sanofi$Day15pseudoneutid50_BA.4.BA.5 - dat.sanofi$Bpseudoneutid50_BA.4.BA.5
dat.sanofi$Day15overBpseudoneutid50_D614G = dat.sanofi$Day15pseudoneutid50_D614G - dat.sanofi$Bpseudoneutid50_D614G
dat.ocp$Day15overBpseudoneutid50_BA.4.BA.5 = dat.ocp$Day15pseudoneutid50_BA.4.BA.5 - dat.ocp$Bpseudoneutid50_BA.4.BA.5
dat.ocp$Day15overBpseudoneutid50_D614G = dat.ocp$Day15pseudoneutid50_D614G - dat.ocp$Bpseudoneutid50_D614G
dat.sanofi$Day29overBpseudoneutid50_BA.4.BA.5 = dat.sanofi$Day29pseudoneutid50_BA.4.BA.5 - dat.sanofi$Bpseudoneutid50_BA.4.BA.5
dat.sanofi$Day29overBpseudoneutid50_D614G = dat.sanofi$Day29pseudoneutid50_D614G - dat.sanofi$Bpseudoneutid50_D614G
dat.ocp$Day29overBpseudoneutid50_BA.4.BA.5 = dat.ocp$Day29pseudoneutid50_BA.4.BA.5 - dat.ocp$Bpseudoneutid50_BA.4.BA.5
dat.ocp$Day29overBpseudoneutid50_D614G = dat.ocp$Day29pseudoneutid50_D614G - dat.ocp$Bpseudoneutid50_D614G

Correlation between D15 over D1 fold change in ancestral and BA4BA5 ID50.

par(mfrow=c(1,3))
lim1=c(0,3.3)
corplot(Day15overBpseudoneutid50_BA.4.BA.5~Day15overBpseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)"), asp=1, xlim=lim1, ylim=lim1, main="Sanofi Prototype Naive")
corplot(Day15overBpseudoneutid50_BA.4.BA.5~Day15overBpseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)" & Day15overBpseudoneutid50_D614G<3), asp=1, xlim=lim1, ylim=lim1, main="Sanofi Beta-containing Naive")
corplot(Day15overBpseudoneutid50_BA.4.BA.5~Day15overBpseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0), asp=1, xlim=lim1, ylim=lim1, main="Pfz,P, naive")

D29 over D1

par(mfrow=c(1,3))
lim1=c(0,3.3)
corplot(Day29overBpseudoneutid50_BA.4.BA.5~Day29overBpseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)"), asp=1, xlim=lim1, ylim=lim1, main="Sanofi Prototype Naive")
corplot(Day29overBpseudoneutid50_BA.4.BA.5~Day29overBpseudoneutid50_D614G, subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)" & Day29overBpseudoneutid50_D614G<3), asp=1, xlim=lim1, ylim=lim1, main="Sanofi Beta-containing Naive")
corplot(Day29overBpseudoneutid50_BA.4.BA.5~Day29overBpseudoneutid50_D614G, subset(dat.ocp, naive==1 & company=="Pfz" & Trt==0), asp=1, xlim=lim1, ylim=lim1, main="Pfz,P, naive")

comparing fold change between different Sanofi arms

par(mfrow=c(1,2))
myboxplot(list(
  subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)", Day15overBpseudoneutid50_BA.4.BA.5, drop=T),
  subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)", Day15overBpseudoneutid50_BA.4.BA.5, drop=T)), test="w", names=c("Prototype", "Non-prototype"))

myboxplot(list(
  subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)", Day15overBpseudoneutid50_D614G, drop=T),
  subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)", Day15overBpseudoneutid50_D614G, drop=T)), test="w", names=c("Prototype", "Non-prototype"))

Comparing D29 and D15. Quite comparable

par(mfrow=c(1,2))
lim1=NULL
corplot(Day29pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_BA.4.BA.5, subset(dat.sanofi, naive==1 & treatment_actual=="Prototype (Sanofi)"), asp=1, xlim=lim1, ylim=lim1, main="Sanofi,P Naive")
corplot(Day29pseudoneutid50_BA.4.BA.5~Day15pseudoneutid50_BA.4.BA.5, subset(dat.sanofi, naive==1 & treatment_actual!="Prototype (Sanofi)"), asp=1, xlim=lim1, ylim=lim1, main="Sanofi,NP Naive")

correlation between m15 and baseline markers

# mypairs(dat[,paste0("B",assays)])

# mypairs(dat[,paste0("Day15",assays)])

# mypairs(dat[,paste0(c("B","Day15", "Delta15overB"),assays[1])])

marker missingness

table(dat_proc$AsympInfectIndD15to29, dat_proc$ph1.D15)
##    
##        0    1
##   0  110 1116
##   1    3   11
table(dat_proc$arm, dat_proc$ph1.D15)
##     
##        0   1
##   1    1  96
##   2    3 109
##   3   85   0
##   4    2  98
##   5    3  96
##   6    4  92
##   7    0  47
##   8    1  50
##   9    1  52
##   10   2  49
##   11   2  49
##   12   0  52
##   13   1  45
##   14   2  48
##   15   1  49
##   16   2  98
##   17   3  97
table(dat_mapped$ph1.D15, dat_mapped$Immunemarkerset, dat_mapped$arm==3)
## , ,  = FALSE
## 
##    
##        0    1
##   0   49    0
##   1    0 1127
## 
## , ,  = TRUE
## 
##    
##        0    1
##   0    1   85
##   1    0    0
# across assays, all or none
summary(subset(dat_mapped, ph1.D15==1)["Day15"%.%assays[1:5]])
##  Day15pseudoneutid50_D614G Day15pseudoneutid50_Delta Day15pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301             Min.   :1.301           
##  1st Qu.:4.039             1st Qu.:3.739             1st Qu.:3.643           
##  Median :4.348             Median :4.069             Median :4.035           
##  Mean   :4.311             Mean   :4.050             Mean   :3.999           
##  3rd Qu.:4.627             3rd Qu.:4.396             3rd Qu.:4.414           
##  Max.   :5.666             Max.   :5.381             Max.   :5.592           
##                                                                              
##  Day15pseudoneutid50_BA.1 Day15pseudoneutid50_BA.4.BA.5
##  Min.   :1.301            Min.   :1.301                
##  1st Qu.:3.238            1st Qu.:2.954                
##  Median :3.636            Median :3.379                
##  Mean   :3.615            Mean   :3.335                
##  3rd Qu.:4.050            3rd Qu.:3.786                
##  Max.   :5.225            Max.   :5.361                
##                           NA's   :666
summary(subset(dat_mapped, ph1.D15==1)["Day29"%.%assays[1:5]])
##  Day29pseudoneutid50_D614G Day29pseudoneutid50_Delta Day29pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301             Min.   :1.301           
##  1st Qu.:3.985             1st Qu.:3.687             1st Qu.:3.544           
##  Median :4.281             Median :4.002             Median :3.938           
##  Mean   :4.265             Mean   :3.993             Mean   :3.912           
##  3rd Qu.:4.570             3rd Qu.:4.320             3rd Qu.:4.312           
##  Max.   :5.605             Max.   :5.402             Max.   :5.414           
##  NA's   :15                NA's   :15                NA's   :15              
##  Day29pseudoneutid50_BA.1 Day29pseudoneutid50_BA.4.BA.5
##  Min.   :1.301            Min.   :1.301                
##  1st Qu.:3.114            1st Qu.:2.889                
##  Median :3.513            Median :3.272                
##  Mean   :3.482            Mean   :3.232                
##  3rd Qu.:3.894            3rd Qu.:3.649                
##  Max.   :5.326            Max.   :4.907                
##  NA's   :16               NA's   :15
summary(subset(dat_mapped, ph1.D15==1)["Day91"%.%assays[1:5]])
##  Day91pseudoneutid50_D614G Day91pseudoneutid50_Delta Day91pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301             Min.   :1.301           
##  1st Qu.:3.768             1st Qu.:3.474             1st Qu.:3.337           
##  Median :4.115             Median :3.818             Median :3.729           
##  Mean   :4.100             Mean   :3.807             Mean   :3.724           
##  3rd Qu.:4.457             3rd Qu.:4.164             3rd Qu.:4.170           
##  Max.   :5.624             Max.   :5.438             Max.   :5.420           
##  NA's   :27                NA's   :27                NA's   :27              
##  Day91pseudoneutid50_BA.1 Day91pseudoneutid50_BA.4.BA.5
##  Min.   :1.301            Min.   :1.301                
##  1st Qu.:2.937            1st Qu.:2.715                
##  Median :3.396            Median :3.169                
##  Mean   :3.337            Mean   :3.121                
##  3rd Qu.:3.779            3rd Qu.:3.611                
##  Max.   :5.190            Max.   :4.975                
##  NA's   :27               NA's   :27
summary(subset(dat_mapped, ph1.D15==1)["Day181"%.%assays[1:5]])
##  Day181pseudoneutid50_D614G Day181pseudoneutid50_Delta
##  Min.   :1.301              Min.   :1.301             
##  1st Qu.:3.639              1st Qu.:3.282             
##  Median :3.980              Median :3.646             
##  Mean   :3.960              Mean   :3.617             
##  3rd Qu.:4.338              3rd Qu.:3.970             
##  Max.   :5.601              Max.   :5.118             
##  NA's   :59                 NA's   :59                
##  Day181pseudoneutid50_Beta Day181pseudoneutid50_BA.1
##  Min.   :1.301             Min.   :1.301            
##  1st Qu.:3.135             1st Qu.:2.852            
##  Median :3.602             Median :3.286            
##  Mean   :3.551             Mean   :3.229            
##  3rd Qu.:3.997             3rd Qu.:3.738            
##  Max.   :5.298             Max.   :5.228            
##  NA's   :59                NA's   :59               
##  Day181pseudoneutid50_BA.4.BA.5
##  Min.   :1.301                 
##  1st Qu.:2.603                 
##  Median :3.124                 
##  Mean   :3.056                 
##  3rd Qu.:3.591                 
##  Max.   :4.913                 
##  NA's   :59
summary(subset(dat_proc, ph1.D15 & is.na(Day29pseudoneutid50_D614G))["Day29"%.%assays[1:5]])
##  Day29pseudoneutid50_D614G Day29pseudoneutid50_Delta Day29pseudoneutid50_Beta
##  Min.   : NA               Min.   : NA               Min.   : NA             
##  1st Qu.: NA               1st Qu.: NA               1st Qu.: NA             
##  Median : NA               Median : NA               Median : NA             
##  Mean   :NaN               Mean   :NaN               Mean   :NaN             
##  3rd Qu.: NA               3rd Qu.: NA               3rd Qu.: NA             
##  Max.   : NA               Max.   : NA               Max.   : NA             
##  NA's   :15                NA's   :15                NA's   :15              
##  Day29pseudoneutid50_BA.1 Day29pseudoneutid50_BA.4.BA.5
##  Min.   : NA              Min.   : NA                  
##  1st Qu.: NA              1st Qu.: NA                  
##  Median : NA              Median : NA                  
##  Mean   :NaN              Mean   :NaN                  
##  3rd Qu.: NA              3rd Qu.: NA                  
##  Max.   : NA              Max.   : NA                  
##  NA's   :15               NA's   :15
summary(subset(dat_proc, ph1.D15 & is.na(Day91pseudoneutid50_D614G))["Day91"%.%assays[1:5]])
##  Day91pseudoneutid50_D614G Day91pseudoneutid50_Delta Day91pseudoneutid50_Beta
##  Min.   : NA               Min.   : NA               Min.   : NA             
##  1st Qu.: NA               1st Qu.: NA               1st Qu.: NA             
##  Median : NA               Median : NA               Median : NA             
##  Mean   :NaN               Mean   :NaN               Mean   :NaN             
##  3rd Qu.: NA               3rd Qu.: NA               3rd Qu.: NA             
##  Max.   : NA               Max.   : NA               Max.   : NA             
##  NA's   :27                NA's   :27                NA's   :27              
##  Day91pseudoneutid50_BA.1 Day91pseudoneutid50_BA.4.BA.5
##  Min.   : NA              Min.   : NA                  
##  1st Qu.: NA              1st Qu.: NA                  
##  Median : NA              Median : NA                  
##  Mean   :NaN              Mean   :NaN                  
##  3rd Qu.: NA              3rd Qu.: NA                  
##  Max.   : NA              Max.   : NA                  
##  NA's   :27               NA's   :27
summary(subset(dat_proc, ph1.D15 & is.na(Day181pseudoneutid50_D614G))["Day181"%.%assays[1:5]])
##  Day181pseudoneutid50_D614G Day181pseudoneutid50_Delta
##  Min.   : NA                Min.   : NA               
##  1st Qu.: NA                1st Qu.: NA               
##  Median : NA                Median : NA               
##  Mean   :NaN                Mean   :NaN               
##  3rd Qu.: NA                3rd Qu.: NA               
##  Max.   : NA                Max.   : NA               
##  NA's   :59                 NA's   :59                
##  Day181pseudoneutid50_Beta Day181pseudoneutid50_BA.1
##  Min.   : NA               Min.   : NA              
##  1st Qu.: NA               1st Qu.: NA              
##  Median : NA               Median : NA              
##  Mean   :NaN               Mean   :NaN              
##  3rd Qu.: NA               3rd Qu.: NA              
##  Max.   : NA               Max.   : NA              
##  NA's   :59                NA's   :59               
##  Day181pseudoneutid50_BA.4.BA.5
##  Min.   : NA                   
##  1st Qu.: NA                   
##  Median : NA                   
##  Mean   :NaN                   
##  3rd Qu.: NA                   
##  Max.   : NA                   
##  NA's   :59
dat_proc$kp = dat_proc$ph1.D15==1 & dat_proc$COVIDIndD22toend!=1 & dat_proc$AsympInfectIndD15to271!=1 
dat_proc$kp = dat_proc$ph1.D15==1 
for (i in 1:1) {
  with(dat_proc[dat_proc$kp,], print(table(!is.na(get("Day29"%.%assays[i])), !is.na(get("Day15"%.%assays[i])))))
  with(dat_proc[dat_proc$kp,], print(table(!is.na(get("Day91"%.%assays[i])), !is.na(get("Day15"%.%assays[i])))))
  with(dat_proc[dat_proc$kp,], print(table(!is.na(get("Day181"%.%assays[i])), !is.na(get("Day15"%.%assays[i])))))
}
##        
##         TRUE
##   FALSE   15
##   TRUE  1112
##        
##         TRUE
##   FALSE   27
##   TRUE  1100
##        
##         TRUE
##   FALSE   59
##   TRUE  1068
myboxplot(
list(dat_proc$Day15pseudoneutid50_MDW[dat_proc$treatment_actual=="Omicron + Wildtype/Prototype (Pfizer 1)"], 
     dat_proc$Day15pseudoneutid50_MDW[dat_proc$treatment_actual=="1 Dose Omicron + Prototype (Moderna)"])
)

myboxplot(
  list(dat_proc$Day15pseudoneutid50_D614G[dat_proc$treatment_actual=="Omicron + Wildtype/Prototype (Pfizer 1)"], 
       dat_proc$Day15pseudoneutid50_D614G[dat_proc$treatment_actual=="1 Dose Omicron + Prototype (Moderna)"])
)

# my.interaction.plot(subset(dat_proc, ph1==1, 
#                            c(Bpseudoneutid50_BA.1, Day15pseudoneutid50_BA.1)), 
#                     x.ori = 0, xaxislabels = c("B", "D15"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  
# 
# my.interaction.plot(subset(dat_proc, ph1==1, 
#                            c(Day15pseudoneutid50_BA.1, Day29pseudoneutid50_BA.1)), 
#                     x.ori = 1, xaxislabels = c("D15", "D29"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  
# 
# my.interaction.plot(subset(dat_proc, ph1==1, 
#                            c(Day29pseudoneutid50_BA.1, Day91pseudoneutid50_BA.1)), 
#                     x.ori = 2, xaxislabels = c("D29", "D91"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  
# 
# my.interaction.plot(subset(dat_proc, ph1==1, 
#                            c(Day91pseudoneutid50_BA.1, Day181pseudoneutid50_BA.1)), 
#                     x.ori = 3, xaxislabels = c("D91", "D181"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  
# 

marker level over time

par(mfrow=c(4,1), mar=c(2,4,1,1))

dat_proc$ph1 = dat_proc$ph1.D15==1 & dat_proc$COVIDIndD22toend!=1 & dat_proc$AsympInfectIndD15to181!=1 & dat_proc$AsympInfectIndD182to271!=1

plot(0,0,type='n', xlim=c(1,5), ylim=c(1,5), xaxt="n", xlab="", ylab="ID50_BA.1")

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Bpseudoneutid50_BA.1, Day15pseudoneutid50_BA.1)), 
                    x.ori = 0, xaxislabels = c("B", "D15"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day15pseudoneutid50_BA.1, Day29pseudoneutid50_BA.1)), 
                    x.ori = 1, xaxislabels = c("D15", "D29"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day29pseudoneutid50_BA.1, Day91pseudoneutid50_BA.1)), 
                    x.ori = 2, xaxislabels = c("D29", "D91"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day91pseudoneutid50_BA.1, Day181pseudoneutid50_BA.1)), 
                    x.ori = 3, xaxislabels = c("D91", "D181"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  


plot(0,0,type='n', xlim=c(1,5), ylim=c(1,5), xaxt="n", xlab="", ylab="ID50_BA.1")

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Bpseudoneutid50_BA.1, Day15pseudoneutid50_BA.1)), 
                    x.ori = 0, xaxislabels = c("B", "D15"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day15pseudoneutid50_BA.1, Day29pseudoneutid50_BA.1)), 
                    x.ori = 1, xaxislabels = c("D15", "D29"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day29pseudoneutid50_BA.1, Day91pseudoneutid50_BA.1)), 
                    x.ori = 2, xaxislabels = c("D29", "D91"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day91pseudoneutid50_BA.1, Day181pseudoneutid50_BA.1)), 
                    x.ori = 3, xaxislabels = c("D91", "D181"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  



dat_proc$ph1 = dat_proc$ph1.D92 & dat_proc$ph1.D15==1 & dat_proc$COVIDIndD22toend!=1 & dat_proc$AsympInfectIndD15to181!=1 & dat_proc$AsympInfectIndD182to271!=1

plot(0,0,type='n', xlim=c(1,5), ylim=c(1,5), xaxt="n", xlab="", ylab="ID50_BA.1")

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Bpseudoneutid50_BA.1, Day15pseudoneutid50_BA.1)), 
                    x.ori = 0, xaxislabels = c("B", "D15"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day15pseudoneutid50_BA.1, Day29pseudoneutid50_BA.1)), 
                    x.ori = 1, xaxislabels = c("D15", "D29"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day29pseudoneutid50_BA.1, Day91pseudoneutid50_BA.1)), 
                    x.ori = 2, xaxislabels = c("D29", "D91"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1<1.5, 
                           c(Day91pseudoneutid50_BA.1, Day181pseudoneutid50_BA.1)), 
                    x.ori = 3, xaxislabels = c("D91", "D181"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  


plot(0,0,type='n', xlim=c(1,5), ylim=c(1,5), xaxt="n", xlab="", ylab="ID50_BA.1")

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Bpseudoneutid50_BA.1, Day15pseudoneutid50_BA.1)), 
                    x.ori = 0, xaxislabels = c("B", "D15"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day15pseudoneutid50_BA.1, Day29pseudoneutid50_BA.1)), 
                    x.ori = 1, xaxislabels = c("D15", "D29"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day29pseudoneutid50_BA.1, Day91pseudoneutid50_BA.1)), 
                    x.ori = 2, xaxislabels = c("D29", "D91"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

my.interaction.plot(subset(dat_proc, ph1==1 & Bpseudoneutid50_BA.1>1.5, 
                           c(Day91pseudoneutid50_BA.1, Day181pseudoneutid50_BA.1)), 
                    x.ori = 3, xaxislabels = c("D91", "D181"), cex.axis = 1, add = T, xlab = "", ylab = "", pcol = NULL, lcol = NULL)  

sum(dat_proc$ph1.D15==1)
## [1] 1127
dat_proc$kp = dat_proc$ph1.D15==1 & dat_proc$COVIDIndD22toend!=1 & dat_proc$AsympInfectIndD15to271!=1 &
  !is.na(dat_proc$Day29pseudoneutid50_D614G) & !is.na(dat_proc$Day91pseudoneutid50_D614G) & !is.na(dat_proc$Day181pseudoneutid50_D614G) 

nrow(subset(dat_proc, kp))
## [1] 733
nrow(subset(dat_proc, kp & Bpseudoneutid50_BA.1>1.5))
## [1] 619
nrow(subset(dat_proc, kp & Bpseudoneutid50_BA.1<1.5))
## [1] 114

Misc

myboxplot(dat_mapped[, c("B"%.%assays[1:5], "Day15"%.%assays[1:5])], names=sub("pseudoneutid50_", "", rep(assays[1:5],2)))

summary(dat_mapped)
##   Subjectid         EthnicityHispanic EthnicityNotreported     race          
##  Length:1262        Min.   :0.00000   Min.   :0.0000000    Length:1262       
##  Class :character   1st Qu.:0.00000   1st Qu.:0.0000000    Class :character  
##  Mode  :character   Median :0.00000   Median :0.0000000    Mode  :character  
##                     Mean   :0.09113   Mean   :0.0007924                      
##                     3rd Qu.:0.00000   3rd Qu.:0.0000000                      
##                     Max.   :1.00000   Max.   :1.0000000                      
##                                                                              
##      Asian            Black            NatAmer            PacIsl        
##  Min.   :0.0000   Min.   :0.00000   Min.   :0.00000   Min.   :0.000000  
##  1st Qu.:0.0000   1st Qu.:0.00000   1st Qu.:0.00000   1st Qu.:0.000000  
##  Median :0.0000   Median :0.00000   Median :0.00000   Median :0.000000  
##  Mean   :0.1173   Mean   :0.09033   Mean   :0.01426   Mean   :0.001585  
##  3rd Qu.:0.0000   3rd Qu.:0.00000   3rd Qu.:0.00000   3rd Qu.:0.000000  
##  Max.   :1.0000   Max.   :1.00000   Max.   :1.00000   Max.   :1.000000  
##                                                                         
##      White         Multiracial         Unknown              Age       
##  Min.   :0.0000   Min.   :0.00000   Min.   :0.000000   Min.   :18.00  
##  1st Qu.:1.0000   1st Qu.:0.00000   1st Qu.:0.000000   1st Qu.:33.00  
##  Median :1.0000   Median :0.00000   Median :0.000000   Median :45.00  
##  Mean   :0.8035   Mean   :0.03487   Mean   :0.009509   Mean   :47.66  
##  3rd Qu.:1.0000   3rd Qu.:0.00000   3rd Qu.:0.000000   3rd Qu.:65.00  
##  Max.   :1.0000   Max.   :1.00000   Max.   :1.000000   Max.   :85.00  
##                                                                       
##      Age65C          State               City                Sex        
##  Min.   :0.0000   Length:1262        Length:1262        Min.   :0.0000  
##  1st Qu.:0.0000   Class :character   Class :character   1st Qu.:0.0000  
##  Median :0.0000   Mode  :character   Mode  :character   Median :1.0000  
##  Mean   :0.2647                                         Mean   :0.5452  
##  3rd Qu.:1.0000                                         3rd Qu.:1.0000  
##  Max.   :1.0000                                         Max.   :1.0000  
##                                                                         
##      naive        eligibility_deviation early_term_date    oos_boost_date    
##  Min.   :0.0000   Length:1262           Length:1262        Length:1262       
##  1st Qu.:0.0000   Class :character      Class :character   Class :character  
##  Median :1.0000   Mode  :character      Mode  :character   Mode  :character  
##  Mean   :0.6513                                                              
##  3rd Qu.:1.0000                                                              
##  Max.   :1.0000                                                              
##                                                                              
##      RESULT        RESULT_limit          UNITS              ASSAY          
##  Min.   :   41.0   Length:1262        Length:1262        Length:1262       
##  1st Qu.:  251.5   Class :character   Class :character   Class :character  
##  Median :  646.0   Mode  :character   Mode  :character   Mode  :character  
##  Mean   : 2117.9                                                           
##  3rd Qu.: 2093.8                                                           
##  Max.   :48003.0                                                           
##  NA's   :238                                                               
##      stage       treatment_actual   treatment_assigned  stratalab        
##  Min.   :1.000   Length:1262        Length:1262        Length:1262       
##  1st Qu.:1.000   Class :character   Class :character   Class :character  
##  Median :2.000   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :1.966                                                           
##  3rd Qu.:3.000                                                           
##  Max.   :4.000                                                           
##                                                                          
##  primary_vax1_date  primary_vax2_date  pre_study_booster_date
##  Length:1262        Length:1262        Length:1262           
##  Class :character   Class :character   Class :character      
##  Mode  :character   Mode  :character   Mode  :character      
##                                                              
##                                                              
##                                                              
##                                                              
##  primary_booster_type pre_study_infect_date studydose1date    
##  Length:1262          Length:1262           Length:1262       
##  Class :character     Class :character      Class :character  
##  Mode  :character     Mode  :character      Mode  :character  
##                                                               
##                                                               
##                                                               
##                                                               
##  studydose2date      early_term         oos_boost         infect_date1      
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  infect_date2       symptomatic_infect1 symptomatic_infect2  NAntibody        
##  Length:1262        Length:1262         Length:1262         Length:1262       
##  Class :character   Class :character    Class :character    Class :character  
##  Mode  :character   Mode  :character    Mode  :character    Mode  :character  
##                                                                               
##                                                                               
##                                                                               
##                                                                               
##   CTSTAT_SWAB1 CTVALUE_SWAB1   ASSSTAT_SWAB1   ASSQC_SWAB1       
##  Min.   :1     Min.   :14.00   Min.   :1.000   Length:1262       
##  1st Qu.:1     1st Qu.:19.70   1st Qu.:1.000   Class :character  
##  Median :1     Median :22.40   Median :1.000   Mode  :character  
##  Mean   :1     Mean   :22.80   Mean   :1.022                     
##  3rd Qu.:1     3rd Qu.:25.75   3rd Qu.:1.000                     
##  Max.   :1     Max.   :32.80   Max.   :2.000                     
##  NA's   :983   NA's   :983     NA's   :983                       
##  TOTREADS_SWAB1   COVRDPCT_SWAB1  HSTRDPCT_SWAB1   BACRDPCT_SWAB1   
##  Min.   : 38148   Min.   : 5.64   Min.   : 0.000   Min.   : 0.0000  
##  1st Qu.:239706   1st Qu.:95.51   1st Qu.: 0.040   1st Qu.: 0.0600  
##  Median :317509   Median :97.23   Median : 0.140   Median : 0.1100  
##  Mean   :312744   Mean   :95.57   Mean   : 1.228   Mean   : 0.3963  
##  3rd Qu.:383596   3rd Qu.:98.36   3rd Qu.: 0.905   3rd Qu.: 0.3650  
##  Max.   :764242   Max.   :99.22   Max.   :29.430   Max.   :40.7300  
##  NA's   :983      NA's   :983     NA's   :983      NA's   :983      
##  ASSCOMP_SWAB1    PANGOLIN_SWAB1     PANGOVER_SWAB1     SCORCALL_SWAB1    
##  Min.   :0.7400   Length:1262        Length:1262        Length:1262       
##  1st Qu.:0.9900   Class :character   Class :character   Class :character  
##  Median :0.9900   Mode  :character   Mode  :character   Mode  :character  
##  Mean   :0.9834                                                           
##  3rd Qu.:0.9900                                                           
##  Max.   :0.9900                                                           
##  NA's   :983                                                              
##  SCORVER_SWAB1      TRUNCLIN_SWAB1     TRUNCVER_SWAB1     SPKAASUB_SWAB1    
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  SPKAADEL_SWAB1     SPKAAINS_SWAB1 DATE_COLLECT_SWAB1  CTSTAT_SWAB2 
##  Length:1262        Mode:logical   Length:1262        Min.   :1     
##  Class :character   NA's:1262      Class :character   1st Qu.:1     
##  Mode  :character                  Mode  :character   Median :1     
##                                                       Mean   :1     
##                                                       3rd Qu.:1     
##                                                       Max.   :1     
##                                                       NA's   :1261  
##  CTVALUE_SWAB2  ASSSTAT_SWAB2  ASSQC_SWAB2        TOTREADS_SWAB2 
##  Min.   :24.8   Min.   :1      Length:1262        Min.   :94834  
##  1st Qu.:24.8   1st Qu.:1      Class :character   1st Qu.:94834  
##  Median :24.8   Median :1      Mode  :character   Median :94834  
##  Mean   :24.8   Mean   :1                         Mean   :94834  
##  3rd Qu.:24.8   3rd Qu.:1                         3rd Qu.:94834  
##  Max.   :24.8   Max.   :1                         Max.   :94834  
##  NA's   :1261   NA's   :1261                      NA's   :1261   
##  COVRDPCT_SWAB2  HSTRDPCT_SWAB2 BACRDPCT_SWAB2 ASSCOMP_SWAB2 
##  Min.   :97.38   Min.   :0.71   Min.   :0.61   Min.   :0.99  
##  1st Qu.:97.38   1st Qu.:0.71   1st Qu.:0.61   1st Qu.:0.99  
##  Median :97.38   Median :0.71   Median :0.61   Median :0.99  
##  Mean   :97.38   Mean   :0.71   Mean   :0.61   Mean   :0.99  
##  3rd Qu.:97.38   3rd Qu.:0.71   3rd Qu.:0.61   3rd Qu.:0.99  
##  Max.   :97.38   Max.   :0.71   Max.   :0.61   Max.   :0.99  
##  NA's   :1261    NA's   :1261   NA's   :1261   NA's   :1261  
##  PANGOLIN_SWAB2     PANGOVER_SWAB2     SCORCALL_SWAB2     SCORVER_SWAB2     
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  TRUNCLIN_SWAB2     TRUNCVER_SWAB2     SPKAASUB_SWAB2     SPKAADEL_SWAB2    
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  SPKAAINS_SWAB2 DATE_COLLECT_SWAB2    TrtmRNA            arm        
##  Mode:logical   Length:1262        Min.   :0.0000   Min.   : 1.000  
##  NA's:1262      Class :character   1st Qu.:1.0000   1st Qu.: 4.000  
##                 Mode  :character   Median :1.0000   Median : 7.000  
##                                    Mean   :0.8796   Mean   : 8.315  
##                                    3rd Qu.:1.0000   3rd Qu.:13.000  
##                                    Max.   :1.0000   Max.   :17.000  
##                                                                     
##       TrtA             TrtB             TrtC        TrtonedosemRNA  
##  Min.   :0.0000   Min.   :0.0000   Min.   :0.0000   Min.   :0.0000  
##  1st Qu.:0.0000   1st Qu.:0.0000   1st Qu.:1.0000   1st Qu.:1.0000  
##  Median :1.0000   Median :0.0000   Median :1.0000   Median :1.0000  
##  Mean   :0.6624   Mean   :0.1618   Mean   :0.8018   Mean   :0.8114  
##  3rd Qu.:1.0000   3rd Qu.:0.0000   3rd Qu.:1.0000   3rd Qu.:1.0000  
##  Max.   :1.0000   Max.   :1.0000   Max.   :1.0000   Max.   :1.0000  
##  NA's   :643      NA's   :341      NA's   :490                      
##    TrtSanofi      pre_study_booster_until_studydose1_day
##  Min.   :0.0000   Min.   : 11.0                         
##  1st Qu.:0.0000   1st Qu.:164.0                         
##  Median :0.0000   Median :191.0                         
##  Mean   :0.1204   Mean   :207.7                         
##  3rd Qu.:0.0000   3rd Qu.:230.0                         
##  Max.   :1.0000   Max.   :592.0                         
##                                                         
##  pre_study_booster_until_studydose1_day_median
##  Min.   :191                                  
##  1st Qu.:191                                  
##  Median :191                                  
##  Mean   :191                                  
##  3rd Qu.:191                                  
##  Max.   :191                                  
##                                               
##  pre_study_booster_until_studydose1_ind  D1_D15_flag      D1_D29_flag    
##  Min.   :0.0000                         Min.   :0.0000   Min.   :0.0000  
##  1st Qu.:0.0000                         1st Qu.:1.0000   1st Qu.:1.0000  
##  Median :0.0000                         Median :1.0000   Median :1.0000  
##  Mean   :0.4984                         Mean   :0.9818   Mean   :0.9802  
##  3rd Qu.:1.0000                         3rd Qu.:1.0000   3rd Qu.:1.0000  
##  Max.   :1.0000                         Max.   :1.0000   Max.   :1.0000  
##                                                                          
##  Bpseudoneutid50_BA.1 Bpseudoneutid50_Beta Bpseudoneutid50_Delta
##  Min.   :1.301        Min.   :1.301        Min.   :1.301        
##  1st Qu.:2.072        1st Qu.:2.590        1st Qu.:2.904        
##  Median :2.612        Median :3.130        Median :3.357        
##  Mean   :2.583        Mean   :3.072        Mean   :3.315        
##  3rd Qu.:3.181        3rd Qu.:3.606        3rd Qu.:3.775        
##  Max.   :4.681        Max.   :4.917        Max.   :4.893        
##  NA's   :1            NA's   :1            NA's   :1            
##  Bpseudoneutid50Duke_BA.2.12.1 Bpseudoneutid50_BA.4.BA.5 Bpseudoneutid50_D614G
##  Min.   :1.301                 Min.   :1.301             Min.   :1.301        
##  1st Qu.:2.041                 1st Qu.:1.301             1st Qu.:3.257        
##  Median :2.394                 Median :2.425             Median :3.649        
##  Mean   :2.396                 Mean   :2.341             Mean   :3.636        
##  3rd Qu.:2.833                 3rd Qu.:2.990             3rd Qu.:4.096        
##  Max.   :4.235                 Max.   :4.385             Max.   :5.084        
##  NA's   :1137                  NA's   :1                 NA's   :1            
##  Day15pseudoneutid50_BA.1 Day15pseudoneutid50_Beta Day15pseudoneutid50_Delta
##  Min.   :1.301            Min.   :1.301            Min.   :1.301            
##  1st Qu.:3.239            1st Qu.:3.648            1st Qu.:3.734            
##  Median :3.631            Median :4.035            Median :4.067            
##  Mean   :3.613            Mean   :4.000            Mean   :4.044            
##  3rd Qu.:4.053            3rd Qu.:4.415            3rd Qu.:4.391            
##  Max.   :5.225            Max.   :5.592            Max.   :5.381            
##  NA's   :22               NA's   :22               NA's   :22               
##  Day15pseudoneutid50Duke_BA.2.12.1 Day15pseudoneutid50_BA.4.BA.5
##  Min.   :1.301                     Min.   :1.301                
##  1st Qu.:3.078                     1st Qu.:2.952                
##  Median :3.382                     Median :3.380                
##  Mean   :3.390                     Mean   :3.335                
##  3rd Qu.:3.695                     3rd Qu.:3.784                
##  Max.   :4.859                     Max.   :5.361                
##  NA's   :1137                      NA's   :791                  
##  Day15pseudoneutid50_D614G Day29pseudoneutid50_BA.1 Day29pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301            Min.   :1.301           
##  1st Qu.:4.035             1st Qu.:3.119            1st Qu.:3.546           
##  Median :4.343             Median :3.514            Median :3.931           
##  Mean   :4.307             Mean   :3.485            Mean   :3.913           
##  3rd Qu.:4.627             3rd Qu.:3.898            3rd Qu.:4.324           
##  Max.   :5.666             Max.   :5.326            Max.   :5.414           
##  NA's   :22                NA's   :25               NA's   :24              
##  Day29pseudoneutid50_Delta Day29pseudoneutid50_BA.4.BA.5
##  Min.   :1.301             Min.   :1.301                
##  1st Qu.:3.679             1st Qu.:2.889                
##  Median :3.998             Median :3.267                
##  Mean   :3.988             Mean   :3.229                
##  3rd Qu.:4.320             3rd Qu.:3.644                
##  Max.   :5.402             Max.   :4.907                
##  NA's   :24                NA's   :24                   
##  Day29pseudoneutid50_D614G Day91pseudoneutid50_BA.1 Day91pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301            Min.   :1.301           
##  1st Qu.:3.968             1st Qu.:2.948            1st Qu.:3.349           
##  Median :4.278             Median :3.400            Median :3.739           
##  Mean   :4.256             Mean   :3.340            Mean   :3.731           
##  3rd Qu.:4.574             3rd Qu.:3.779            3rd Qu.:4.179           
##  Max.   :5.605             Max.   :5.190            Max.   :5.420           
##  NA's   :24                NA's   :121              NA's   :121             
##  Day91pseudoneutid50_Delta Day91pseudoneutid50_BA.4.BA.5
##  Min.   :1.301             Min.   :1.301                
##  1st Qu.:3.482             1st Qu.:2.719                
##  Median :3.821             Median :3.187                
##  Mean   :3.815             Mean   :3.126                
##  3rd Qu.:4.180             3rd Qu.:3.615                
##  Max.   :5.438             Max.   :4.975                
##  NA's   :121               NA's   :121                  
##  Day91pseudoneutid50_D614G Day181pseudoneutid50_BA.1 Day181pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301             Min.   :1.301            
##  1st Qu.:3.772             1st Qu.:2.855             1st Qu.:3.155            
##  Median :4.122             Median :3.297             Median :3.614            
##  Mean   :4.107             Mean   :3.237             Mean   :3.561            
##  3rd Qu.:4.459             3rd Qu.:3.749             3rd Qu.:4.021            
##  Max.   :5.624             Max.   :5.228             Max.   :5.298            
##  NA's   :121               NA's   :157               NA's   :157              
##  Day181pseudoneutid50_Delta Day181pseudoneutid50_BA.4.BA.5
##  Min.   :1.301              Min.   :1.301                 
##  1st Qu.:3.289              1st Qu.:2.612                 
##  Median :3.657              Median :3.154                 
##  Mean   :3.623              Mean   :3.065                 
##  3rd Qu.:3.991              3rd Qu.:3.599                 
##  Max.   :5.118              Max.   :4.913                 
##  NA's   :157                NA's   :157                   
##  Day181pseudoneutid50_D614G Day85pseudoneutid50_BA.1 Day85pseudoneutid50_Beta
##  Min.   :1.301              Min.   :1.301            Min.   :1.301           
##  1st Qu.:3.656              1st Qu.:3.289            1st Qu.:3.646           
##  Median :3.993              Median :3.574            Median :4.078           
##  Mean   :3.966              Mean   :3.614            Mean   :4.012           
##  3rd Qu.:4.346              3rd Qu.:4.009            3rd Qu.:4.365           
##  Max.   :5.601              Max.   :4.837            Max.   :5.144           
##  NA's   :157                NA's   :1177             NA's   :1177            
##  Day85pseudoneutid50_Delta Day85pseudoneutid50_BA.4.BA.5
##  Min.   :1.301             Min.   :1.301                
##  1st Qu.:3.710             1st Qu.:2.982                
##  Median :3.942             Median :3.215                
##  Mean   :3.994             Mean   :3.307                
##  3rd Qu.:4.365             3rd Qu.:3.709                
##  Max.   :5.082             Max.   :4.623                
##  NA's   :1177              NA's   :1177                 
##  Day85pseudoneutid50_D614G Day147pseudoneutid50_BA.1 Day147pseudoneutid50_Beta
##  Min.   :1.301             Min.   :1.301             Min.   :1.301            
##  1st Qu.:3.892             1st Qu.:3.030             1st Qu.:3.255            
##  Median :4.189             Median :3.384             Median :3.721            
##  Mean   :4.213             Mean   :3.418             Mean   :3.704            
##  3rd Qu.:4.557             3rd Qu.:3.886             3rd Qu.:4.092            
##  Max.   :5.179             Max.   :4.796             Max.   :4.740            
##  NA's   :1177              NA's   :1176              NA's   :1176             
##  Day147pseudoneutid50_Delta Day147pseudoneutid50_BA.4.BA.5
##  Min.   :1.301              Min.   :1.301                 
##  1st Qu.:3.369              1st Qu.:2.616                 
##  Median :3.694              Median :3.070                 
##  Mean   :3.700              Mean   :3.078                 
##  3rd Qu.:4.130              3rd Qu.:3.696                 
##  Max.   :4.803              Max.   :4.481                 
##  NA's   :1176               NA's   :1176                  
##  Day147pseudoneutid50_D614G symptm_infect1   symptm_infect1_date
##  Min.   :1.301              Min.   :0.0000   Length:1262        
##  1st Qu.:3.630              1st Qu.:0.0000   Class :character   
##  Median :3.984              Median :0.0000   Mode  :character   
##  Mean   :3.999              Mean   :0.2979                      
##  3rd Qu.:4.373              3rd Qu.:1.0000                      
##  Max.   :4.963              Max.   :1.0000                      
##  NA's   :1176                                                   
##   N_status_1.0    N_status_15.2 N_status_181.14 N_status_271.14 
##  Min.   :0.0000   Min.   :0     Min.   :0.000   Min.   :0.0000  
##  1st Qu.:0.0000   1st Qu.:0     1st Qu.:0.000   1st Qu.:0.0000  
##  Median :0.0000   Median :0     Median :1.000   Median :1.0000  
##  Mean   :0.3315   Mean   :0     Mean   :0.552   Mean   :0.5795  
##  3rd Qu.:1.0000   3rd Qu.:0     3rd Qu.:1.000   3rd Qu.:1.0000  
##  Max.   :1.0000   Max.   :0     Max.   :1.000   Max.   :1.0000  
##  NA's   :1        NA's   :22    NA's   :157     NA's   :375     
##  N_status_29.2    N_status_91.7    Actual_visit_date_1.0 Actual_visit_date_15.2
##  Min.   :0.0000   Min.   :0.0000   Length:1262           Length:1262           
##  1st Qu.:0.0000   1st Qu.:0.0000   Class :character      Class :character      
##  Median :0.0000   Median :0.0000   Mode  :character      Mode  :character      
##  Mean   :0.3586   Mean   :0.4663                                               
##  3rd Qu.:1.0000   3rd Qu.:1.0000                                               
##  Max.   :1.0000   Max.   :1.0000                                               
##  NA's   :24       NA's   :121                                                  
##  Actual_visit_date_181.14 Actual_visit_date_271.14 Actual_visit_date_29.2
##  Length:1262              Length:1262              Length:1262           
##  Class :character         Class :character         Class :character      
##  Mode  :character         Mode  :character         Mode  :character      
##                                                                          
##                                                                          
##                                                                          
##                                                                          
##  Actual_visit_date_91.7 first_Npos_date    Target_study_day_numeric
##  Length:1262            Length:1262        Min.   :  1.00          
##  Class :character       Class :character   1st Qu.:  1.00          
##  Mode  :character       Mode  :character   Median :  1.00          
##                                            Mean   : 71.81          
##                                            3rd Qu.:181.00          
##                                            Max.   :271.00          
##                                            NA's   :497             
##  NumberdaysD15toD29 NumberdaysD15toD91 NumberdaysD15toD181 last_contact_date 
##  Min.   : 6.00      Min.   : 54.00     Min.   : 98.0       Length:1262       
##  1st Qu.:13.00      1st Qu.: 70.00     1st Qu.:154.0       Class :character  
##  Median :14.00      Median : 75.00     Median :159.0       Mode  :character  
##  Mean   :14.18      Mean   : 74.64     Mean   :158.9                         
##  3rd Qu.:15.00      3rd Qu.: 77.00     3rd Qu.:167.0                         
##  Max.   :34.00      Max.   :102.00     Max.   :191.0                         
##  NA's   :38         NA's   :134        NA's   :173                           
##   Perprotocol     symptm_infect1_date_imp oos_boost_date_imp
##  Min.   :0.0000   Length:1262             Length:1262       
##  1st Qu.:1.0000   Class :character        Class :character  
##  Median :1.0000   Mode  :character        Mode  :character  
##  Mean   :0.9794                                             
##  3rd Qu.:1.0000                                             
##  Max.   :1.0000                                             
##                                                             
##  early_term_date_imp EarlyendpointD15  Immunemarkerset 
##  Length:1262         Min.   :0.00000   Min.   :0.0000  
##  Class :character    1st Qu.:0.00000   1st Qu.:1.0000  
##  Mode  :character    Median :0.00000   Median :1.0000  
##                      Mean   :0.01936   Mean   :0.9604  
##                      3rd Qu.:0.00000   3rd Qu.:1.0000  
##                      Max.   :1.00000   Max.   :1.0000  
##                      NA's   :22                        
##  ImmunemarkersetD92toD181    ph1.D15         ph1.D92          ph1.D29      
##  Min.   :0.0000           Min.   :0.000   Min.   :0.0000   Min.   :0.0000  
##  1st Qu.:1.0000           1st Qu.:1.000   1st Qu.:0.0000   1st Qu.:0.0000  
##  Median :1.0000           Median :1.000   Median :1.0000   Median :0.0000  
##  Mean   :0.7971           Mean   :0.893   Mean   :0.7393   Mean   :0.1086  
##  3rd Qu.:1.0000           3rd Qu.:1.000   3rd Qu.:1.0000   3rd Qu.:0.0000  
##  Max.   :1.0000           Max.   :1.000   Max.   :1.0000   Max.   :1.0000  
##                                                                            
##  CNSR1_D22toD91     CNSR1_D92toD181    CNSR1_D22toD181    CNSR1_D36toD181   
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  CNSR1_D22toend        CNSR2              CNSR3              CNSR4          
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##     CNSR5           CNSR_D22toD91      CNSR_D92toD181     CNSR_D22toD181    
##  Length:1262        Length:1262        Length:1262        Length:1262       
##  Class :character   Class :character   Class :character   Class :character  
##  Mode  :character   Mode  :character   Mode  :character   Mode  :character  
##                                                                             
##                                                                             
##                                                                             
##                                                                             
##  CNSR_D36toD181     CNSR_D22toend      COVIDtimeD22toD91 COVIDIndD22toD91
##  Length:1262        Length:1262        Min.   :-14.00    Min.   :0.0000  
##  Class :character   Class :character   1st Qu.: 91.00    1st Qu.:0.0000  
##  Mode  :character   Mode  :character   Median : 91.00    Median :0.0000  
##                                        Mean   : 79.48    Mean   :0.1332  
##                                        3rd Qu.: 91.00    3rd Qu.:0.0000  
##                                        Max.   : 91.00    Max.   :1.0000  
##                                        NA's   :22        NA's   :46      
##  COVIDtimeD92toD181 COVIDIndD92toD181 COVIDtimeD22toD181 COVIDIndD22toD181
##  Min.   :-14.0      Min.   :0.00000   Min.   :-14.0      Min.   :0.0000   
##  1st Qu.: 94.0      1st Qu.:0.00000   1st Qu.: 94.0      1st Qu.:0.0000   
##  Median :171.0      Median :0.00000   Median :171.0      Median :0.0000   
##  Mean   :140.2      Mean   :0.07102   Mean   :140.2      Mean   :0.1941   
##  3rd Qu.:188.0      3rd Qu.:0.00000   3rd Qu.:188.0      3rd Qu.:0.0000   
##  Max.   :188.0      Max.   :1.00000   Max.   :188.0      Max.   :1.0000   
##  NA's   :22         NA's   :220       NA's   :22         NA's   :46       
##  COVIDtimeD36toD181 COVIDIndD36toD181 COVIDIndD22toend AsympInfectIndD15to29
##  Min.   :-27.0      Min.   :0.000     Min.   :0.0000   Min.   :0.00000      
##  1st Qu.: 82.0      1st Qu.:0.000     1st Qu.:0.0000   1st Qu.:0.00000      
##  Median :156.0      Median :0.000     Median :0.0000   Median :0.00000      
##  Mean   :132.3      Mean   :0.179     Mean   :0.2163   Mean   :0.01109      
##  3rd Qu.:188.0      3rd Qu.:0.000     3rd Qu.:0.0000   3rd Qu.:0.00000      
##  Max.   :188.0      Max.   :1.000     Max.   :1.0000   Max.   :1.00000      
##  NA's   :24         NA's   :72        NA's   :46                            
##  AsympInfectIndD30to91 AsympInfectIndD15to91 AsympInfectIndD92to181
##  Min.   :0.00000       Min.   :0.00000       Min.   :0.0000        
##  1st Qu.:0.00000       1st Qu.:0.00000       1st Qu.:0.0000        
##  Median :0.00000       Median :0.00000       Median :0.0000        
##  Mean   :0.01664       Mean   :0.02773       Mean   :0.0206        
##  3rd Qu.:0.00000       3rd Qu.:0.00000       3rd Qu.:0.0000        
##  Max.   :1.00000       Max.   :1.00000       Max.   :1.0000        
##                                                                    
##  AsympInfectIndD182to271 AsympInfectIndD15to181 AsympInfectIndD15to271
##  Min.   :0.00000         Min.   :0.00000        Min.   :0.00000       
##  1st Qu.:0.00000         1st Qu.:0.00000        1st Qu.:0.00000       
##  Median :0.00000         Median :0.00000        Median :0.00000       
##  Mean   :0.01347         Mean   :0.04834        Mean   :0.06181       
##  3rd Qu.:0.00000         3rd Qu.:0.00000        3rd Qu.:0.00000       
##  Max.   :1.00000         Max.   :1.00000        Max.   :1.00000       
##                                                                       
##  Bcd4_154_BA.4.5.S1 Bcd4_154_BA.4.5.S2 Bcd4_154_COV2.CON.S1
##  Min.   :0.0010     Min.   :0.0010     Min.   :0.0010      
##  1st Qu.:0.0277     1st Qu.:0.0390     1st Qu.:0.0434      
##  Median :0.0531     Median :0.0677     Median :0.0688      
##  Mean   :0.0753     Mean   :0.0905     Mean   :0.1005      
##  3rd Qu.:0.0946     3rd Qu.:0.1155     3rd Qu.:0.1159      
##  Max.   :0.6903     Max.   :0.5670     Max.   :0.7643      
##  NA's   :692        NA's   :710        NA's   :686         
##  Bcd4_154_COV2.CON.S2 Bcd4_154_Wuhan.N Bcd4_CXCR5.154_BA.4.5.S1
##  Min.   :0.0010       Min.   :0.0010   Min.   :0.0010          
##  1st Qu.:0.0439       1st Qu.:0.0010   1st Qu.:0.0011          
##  Median :0.0796       Median :0.0069   Median :0.0031          
##  Mean   :0.1026       Mean   :0.0165   Mean   :0.0044          
##  3rd Qu.:0.1308       3rd Qu.:0.0178   3rd Qu.:0.0059          
##  Max.   :0.5934       Max.   :0.4365   Max.   :0.0339          
##  NA's   :686          NA's   :745      NA's   :700             
##  Bcd4_CXCR5.154_BA.4.5.S2 Bcd4_CXCR5.154_COV2.CON.S1 Bcd4_CXCR5.154_COV2.CON.S2
##  Min.   :0.0010           Min.   :0.0010             Min.   :0.0010            
##  1st Qu.:0.0012           1st Qu.:0.0022             1st Qu.:0.0018            
##  Median :0.0032           Median :0.0046             Median :0.0039            
##  Mean   :0.0045           Mean   :0.0065             Mean   :0.0054            
##  3rd Qu.:0.0058           3rd Qu.:0.0086             3rd Qu.:0.0070            
##  Max.   :0.0866           Max.   :0.0477             Max.   :0.1106            
##  NA's   :713              NA's   :687                NA's   :686               
##  Bcd4_CXCR5.154_Wuhan.N Bcd4_CXCR5.IL21_BA.4.5.S1 Bcd4_CXCR5.IL21_BA.4.5.S2
##  Min.   :0.0010         Min.   :0.0010            Min.   :0.0010           
##  1st Qu.:0.0010         1st Qu.:0.0010            1st Qu.:0.0010           
##  Median :0.0010         Median :0.0010            Median :0.0010           
##  Mean   :0.0026         Mean   :0.0017            Mean   :0.0018           
##  3rd Qu.:0.0027         3rd Qu.:0.0019            3rd Qu.:0.0020           
##  Max.   :0.0522         Max.   :0.0135            Max.   :0.0139           
##  NA's   :750            NA's   :700               NA's   :713              
##  Bcd4_CXCR5.IL21_COV2.CON.S1 Bcd4_CXCR5.IL21_COV2.CON.S2
##  Min.   :0.0010              Min.   :0.0010             
##  1st Qu.:0.0010              1st Qu.:0.0010             
##  Median :0.0011              Median :0.0010             
##  Mean   :0.0023              Mean   :0.0019             
##  3rd Qu.:0.0027              3rd Qu.:0.0020             
##  Max.   :0.0174              Max.   :0.0164             
##  NA's   :687                 NA's   :686                
##  Bcd4_CXCR5.IL21_Wuhan.N Bcd4_IFNg_BA.4.5.S1 Bcd4_IFNg_BA.4.5.S2
##  Min.   :0.0010          Min.   :0.0010      Min.   :0.0010     
##  1st Qu.:0.0010          1st Qu.:0.0164      1st Qu.:0.0267     
##  Median :0.0010          Median :0.0334      Median :0.0466     
##  Mean   :0.0014          Mean   :0.0485      Mean   :0.0620     
##  3rd Qu.:0.0010          3rd Qu.:0.0575      3rd Qu.:0.0818     
##  Max.   :0.0395          Max.   :0.7835      Max.   :0.5082     
##  NA's   :750             NA's   :692         NA's   :710        
##  Bcd4_IFNg_COV2.CON.S1 Bcd4_IFNg_COV2.CON.S2 Bcd4_IFNg_Wuhan.N
##  Min.   :0.0010        Min.   :0.0010        Min.   :0.0010   
##  1st Qu.:0.0251        1st Qu.:0.0320        1st Qu.:0.0010   
##  Median :0.0446        Median :0.0556        Median :0.0035   
##  Mean   :0.0634        Mean   :0.0708        Mean   :0.0107   
##  3rd Qu.:0.0748        3rd Qu.:0.0891        3rd Qu.:0.0108   
##  Max.   :0.7517        Max.   :0.5097        Max.   :0.2599   
##  NA's   :686           NA's   :686           NA's   :745      
##  Bcd4_IFNg.IL2_BA.4.5.S1 Bcd4_IFNg.IL2_BA.4.5.S2 Bcd4_IFNg.IL2_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0275          1st Qu.:0.0388          1st Qu.:0.0396           
##  Median :0.0525          Median :0.0728          Median :0.0710           
##  Mean   :0.0798          Mean   :0.0996          Mean   :0.1054           
##  3rd Qu.:0.0931          3rd Qu.:0.1277          3rd Qu.:0.1247           
##  Max.   :0.8216          Max.   :0.7870          Max.   :0.8138           
##  NA's   :692             NA's   :710             NA's   :686              
##  Bcd4_IFNg.IL2_COV2.CON.S2 Bcd4_IFNg.IL2_Wuhan.N Bcd4_IFNg.IL2.154_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010             
##  1st Qu.:0.0478            1st Qu.:0.0010        1st Qu.:0.0317             
##  Median :0.0848            Median :0.0038        Median :0.0604             
##  Mean   :0.1136            Mean   :0.0158        Mean   :0.0896             
##  3rd Qu.:0.1458            3rd Qu.:0.0176        3rd Qu.:0.1094             
##  Max.   :0.7656            Max.   :0.3488        Max.   :0.8375             
##  NA's   :686               NA's   :745           NA's   :692                
##  Bcd4_IFNg.IL2.154_BA.4.5.S2 Bcd4_IFNg.IL2.154_COV2.CON.S1
##  Min.   :0.0010              Min.   :0.0010               
##  1st Qu.:0.0451              1st Qu.:0.0471               
##  Median :0.0817              Median :0.0803               
##  Mean   :0.1103              Mean   :0.1185               
##  3rd Qu.:0.1399              3rd Qu.:0.1404               
##  Max.   :0.8358              Max.   :0.8391               
##  NA's   :710                 NA's   :686                  
##  Bcd4_IFNg.IL2.154_COV2.CON.S2 Bcd4_IFNg.IL2.154_Wuhan.N Bcd4_IL17a_BA.4.5.S1
##  Min.   :0.0010                Min.   :0.0010            Min.   :0.0010      
##  1st Qu.:0.0534                1st Qu.:0.0010            1st Qu.:0.0010      
##  Median :0.0951                Median :0.0048            Median :0.0010      
##  Mean   :0.1256                Mean   :0.0181            Mean   :0.0016      
##  3rd Qu.:0.1624                3rd Qu.:0.0200            3rd Qu.:0.0014      
##  Max.   :0.8387                Max.   :0.4696            Max.   :0.0115      
##  NA's   :686                   NA's   :745               NA's   :692         
##  Bcd4_IL17a_BA.4.5.S2 Bcd4_IL17a_COV2.CON.S1 Bcd4_IL17a_COV2.CON.S2
##  Min.   :0.0010       Min.   :0.0010         Min.   :0.0010        
##  1st Qu.:0.0010       1st Qu.:0.0010         1st Qu.:0.0010        
##  Median :0.0010       Median :0.0010         Median :0.0010        
##  Mean   :0.0015       Mean   :0.0015         Mean   :0.0016        
##  3rd Qu.:0.0011       3rd Qu.:0.0013         3rd Qu.:0.0013        
##  Max.   :0.0104       Max.   :0.0114         Max.   :0.0115        
##  NA's   :710          NA's   :686            NA's   :686           
##  Bcd4_IL17a_Wuhan.N Bcd4_IL2_BA.4.5.S1 Bcd4_IL2_BA.4.5.S2 Bcd4_IL2_COV2.CON.S1
##  Min.   :0.0010     Min.   :0.0010     Min.   :0.0010     Min.   :0.0010      
##  1st Qu.:0.0010     1st Qu.:0.0202     1st Qu.:0.0298     1st Qu.:0.0294      
##  Median :0.0010     Median :0.0431     Median :0.0571     Median :0.0569      
##  Mean   :0.0013     Mean   :0.0672     Mean   :0.0830     Mean   :0.0894      
##  3rd Qu.:0.0010     3rd Qu.:0.0781     3rd Qu.:0.1068     3rd Qu.:0.1022      
##  Max.   :0.0103     Max.   :0.6065     Max.   :0.7696     Max.   :0.7052      
##  NA's   :745        NA's   :692        NA's   :710        NA's   :686         
##  Bcd4_IL2_COV2.CON.S2 Bcd4_IL2_Wuhan.N Bcd4_IL21_BA.4.5.S1 Bcd4_IL21_BA.4.5.S2
##  Min.   :0.0010       Min.   :0.0010   Min.   :0.0010      Min.   :0.0010     
##  1st Qu.:0.0347       1st Qu.:0.0010   1st Qu.:0.0010      1st Qu.:0.0010     
##  Median :0.0654       Median :0.0031   Median :0.0013      Median :0.0027     
##  Mean   :0.0948       Mean   :0.0132   Mean   :0.0039      Mean   :0.0051     
##  3rd Qu.:0.1198       3rd Qu.:0.0147   3rd Qu.:0.0047      3rd Qu.:0.0065     
##  Max.   :0.7439       Max.   :0.3340   Max.   :0.0441      Max.   :0.0679     
##  NA's   :686          NA's   :745      NA's   :692         NA's   :710        
##  Bcd4_IL21_COV2.CON.S1 Bcd4_IL21_COV2.CON.S2 Bcd4_IL21_Wuhan.N
##  Min.   :0.0010        Min.   :0.0010        Min.   :0.0010   
##  1st Qu.:0.0010        1st Qu.:0.0010        1st Qu.:0.0010   
##  Median :0.0030        Median :0.0029        Median :0.0010   
##  Mean   :0.0057        Mean   :0.0057        Mean   :0.0033   
##  3rd Qu.:0.0073        3rd Qu.:0.0073        3rd Qu.:0.0030   
##  Max.   :0.0802        Max.   :0.0612        Max.   :0.1515   
##  NA's   :686           NA's   :686           NA's   :745      
##  Bcd4_IL4.154_BA.4.5.S1 Bcd4_IL4.154_BA.4.5.S2 Bcd4_IL4.154_COV2.CON.S1
##  Min.   :0.0010         Min.   :0.0010         Min.   :0.0010          
##  1st Qu.:0.0010         1st Qu.:0.0010         1st Qu.:0.0010          
##  Median :0.0010         Median :0.0010         Median :0.0010          
##  Mean   :0.0016         Mean   :0.0016         Mean   :0.0018          
##  3rd Qu.:0.0010         3rd Qu.:0.0010         3rd Qu.:0.0013          
##  Max.   :0.0294         Max.   :0.0250         Max.   :0.0276          
##  NA's   :692            NA's   :710            NA's   :686             
##  Bcd4_IL4.154_COV2.CON.S2 Bcd4_IL4.154_Wuhan.N Bcd4_IL4.IL5.IL13.154_BA.4.5.S1
##  Min.   :0.0010           Min.   :0.0010       Min.   :0.0010                 
##  1st Qu.:0.0010           1st Qu.:0.0010       1st Qu.:0.0010                 
##  Median :0.0010           Median :0.0010       Median :0.0010                 
##  Mean   :0.0017           Mean   :0.0010       Mean   :0.0019                 
##  3rd Qu.:0.0012           3rd Qu.:0.0010       3rd Qu.:0.0013                 
##  Max.   :0.0441           Max.   :0.0075       Max.   :0.0330                 
##  NA's   :686              NA's   :745          NA's   :692                    
##  Bcd4_IL4.IL5.IL13.154_BA.4.5.S2 Bcd4_IL4.IL5.IL13.154_COV2.CON.S1
##  Min.   :0.0010                  Min.   :0.0010                   
##  1st Qu.:0.0010                  1st Qu.:0.0010                   
##  Median :0.0010                  Median :0.0010                   
##  Mean   :0.0019                  Mean   :0.0022                   
##  3rd Qu.:0.0013                  3rd Qu.:0.0016                   
##  Max.   :0.0375                  Max.   :0.0329                   
##  NA's   :710                     NA's   :686                      
##  Bcd4_IL4.IL5.IL13.154_COV2.CON.S2 Bcd4_IL4.IL5.IL13.154_Wuhan.N
##  Min.   :0.0010                    Min.   :0.0010               
##  1st Qu.:0.0010                    1st Qu.:0.0010               
##  Median :0.0010                    Median :0.0010               
##  Mean   :0.0020                    Mean   :0.0011               
##  3rd Qu.:0.0014                    3rd Qu.:0.0010               
##  Max.   :0.0573                    Max.   :0.0083               
##  NA's   :686                       NA's   :745                  
##  Bcd4_IL5.IL13.154_BA.4.5.S1 Bcd4_IL5.IL13.154_BA.4.5.S2
##  Min.   :0.0010              Min.   :0.0010             
##  1st Qu.:0.0010              1st Qu.:0.0010             
##  Median :0.0010              Median :0.0010             
##  Mean   :0.0015              Mean   :0.0014             
##  3rd Qu.:0.0010              3rd Qu.:0.0010             
##  Max.   :0.0214              Max.   :0.0236             
##  NA's   :692                 NA's   :710                
##  Bcd4_IL5.IL13.154_COV2.CON.S1 Bcd4_IL5.IL13.154_COV2.CON.S2
##  Min.   :0.0010                Min.   :0.0010               
##  1st Qu.:0.0010                1st Qu.:0.0010               
##  Median :0.0010                Median :0.0010               
##  Mean   :0.0017                Mean   :0.0015               
##  3rd Qu.:0.0010                3rd Qu.:0.0010               
##  Max.   :0.0302                Max.   :0.0338               
##  NA's   :686                   NA's   :686                  
##  Bcd4_IL5.IL13.154_Wuhan.N Bcd4_TNFa_BA.4.5.S1 Bcd4_TNFa_BA.4.5.S2
##  Min.   :0.0010            Min.   :0.0010      Min.   :0.0010     
##  1st Qu.:0.0010            1st Qu.:0.0040      1st Qu.:0.0140     
##  Median :0.0010            Median :0.0409      Median :0.0514     
##  Mean   :0.0010            Mean   :0.0709      Mean   :0.0865     
##  3rd Qu.:0.0010            3rd Qu.:0.0879      3rd Qu.:0.1175     
##  Max.   :0.0039            Max.   :0.8326      Max.   :0.9873     
##  NA's   :745               NA's   :692         NA's   :710        
##  Bcd4_TNFa_COV2.CON.S1 Bcd4_TNFa_COV2.CON.S2 Bcd4_TNFa_Wuhan.N
##  Min.   :0.0010        Min.   :0.0010        Min.   :0.0010   
##  1st Qu.:0.0061        1st Qu.:0.0151        1st Qu.:0.0010   
##  Median :0.0536        Median :0.0620        Median :0.0010   
##  Mean   :0.0883        Mean   :0.0990        Mean   :0.0101   
##  3rd Qu.:0.1105        3rd Qu.:0.1420        3rd Qu.:0.0010   
##  Max.   :0.9469        Max.   :0.9527        Max.   :0.5128   
##  NA's   :686           NA's   :686           NA's   :745      
##  Bcd8_IFNg_BA.4.5.S1 Bcd8_IFNg_BA.4.5.S2 Bcd8_IFNg_COV2.CON.S1
##  Min.   :0.0010      Min.   :0.0010      Min.   : 0.0010      
##  1st Qu.:0.0061      1st Qu.:0.0018      1st Qu.: 0.0062      
##  Median :0.0323      Median :0.0097      Median : 0.0351      
##  Mean   :0.2588      Mean   :0.0538      Mean   : 0.2730      
##  3rd Qu.:0.1269      3rd Qu.:0.0355      3rd Qu.: 0.1464      
##  Max.   :8.9190      Max.   :2.5966      Max.   :10.2187      
##  NA's   :694         NA's   :710         NA's   :686          
##  Bcd8_IFNg_COV2.CON.S2 Bcd8_IFNg_Wuhan.N Bcd8_IFNg.IL2_BA.4.5.S1
##  Min.   :0.0010        Min.   :0.0010    Min.   :0.0010         
##  1st Qu.:0.0011        1st Qu.:0.0010    1st Qu.:0.0064         
##  Median :0.0104        Median :0.0010    Median :0.0343         
##  Mean   :0.0560        Mean   :0.0126    Mean   :0.2605         
##  3rd Qu.:0.0319        3rd Qu.:0.0053    3rd Qu.:0.1280         
##  Max.   :4.9023        Max.   :0.9490    Max.   :8.9239         
##  NA's   :686           NA's   :746       NA's   :694            
##  Bcd8_IFNg.IL2_BA.4.5.S2 Bcd8_IFNg.IL2_COV2.CON.S1 Bcd8_IFNg.IL2_COV2.CON.S2
##  Min.   :0.0010          Min.   : 0.0010           Min.   :0.0010           
##  1st Qu.:0.0011          1st Qu.: 0.0065           1st Qu.:0.0011           
##  Median :0.0102          Median : 0.0360           Median :0.0109           
##  Mean   :0.0538          Mean   : 0.2749           Mean   :0.0563           
##  3rd Qu.:0.0357          3rd Qu.: 0.1461           3rd Qu.:0.0330           
##  Max.   :2.5966          Max.   :10.2283           Max.   :4.9113           
##  NA's   :710             NA's   :686               NA's   :686              
##  Bcd8_IFNg.IL2_Wuhan.N Bcd8_IFNg.IL2.TNFa_BA.4.5.S1
##  Min.   :0.0010        Min.   :0.0010              
##  1st Qu.:0.0010        1st Qu.:0.0075              
##  Median :0.0010        Median :0.0442              
##  Mean   :0.0128        Mean   :0.2722              
##  3rd Qu.:0.0062        3rd Qu.:0.1436              
##  Max.   :0.9464        Max.   :9.6164              
##  NA's   :746           NA's   :694                 
##  Bcd8_IFNg.IL2.TNFa_BA.4.5.S2 Bcd8_IFNg.IL2.TNFa_COV2.CON.S1
##  Min.   :0.0010               Min.   : 0.0010               
##  1st Qu.:0.0010               1st Qu.: 0.0067               
##  Median :0.0123               Median : 0.0374               
##  Mean   :0.0615               Mean   : 0.2861               
##  3rd Qu.:0.0447               3rd Qu.: 0.1563               
##  Max.   :2.6188               Max.   :10.7786               
##  NA's   :710                  NA's   :686                   
##  Bcd8_IFNg.IL2.TNFa_COV2.CON.S2 Bcd8_IFNg.IL2.TNFa_Wuhan.N Bcd8_IL2_BA.4.5.S1
##  Min.   :0.0010                 Min.   :0.0010             Min.   :0.0010    
##  1st Qu.:0.0010                 1st Qu.:0.0010             1st Qu.:0.0010    
##  Median :0.0131                 Median :0.0010             Median :0.0065    
##  Mean   :0.0611                 Mean   :0.0146             Mean   :0.0319    
##  3rd Qu.:0.0393                 3rd Qu.:0.0102             3rd Qu.:0.0249    
##  Max.   :5.1185                 Max.   :0.9392             Max.   :1.0542    
##  NA's   :686                    NA's   :746                NA's   :694       
##  Bcd8_IL2_BA.4.5.S2 Bcd8_IL2_COV2.CON.S1 Bcd8_IL2_COV2.CON.S2 Bcd8_IL2_Wuhan.N
##  Min.   :0.0010     Min.   :0.0010       Min.   :0.0010       Min.   :0.0010  
##  1st Qu.:0.0010     1st Qu.:0.0010       1st Qu.:0.0010       1st Qu.:0.0010  
##  Median :0.0017     Median :0.0070       Median :0.0021       Median :0.0010  
##  Mean   :0.0075     Mean   :0.0296       Mean   :0.0084       Mean   :0.0051  
##  3rd Qu.:0.0062     3rd Qu.:0.0245       3rd Qu.:0.0063       3rd Qu.:0.0026  
##  Max.   :0.2089     Max.   :0.6245       Max.   :0.2640       Max.   :0.3005  
##  NA's   :710        NA's   :686          NA's   :686          NA's   :746     
##  Bcd8_TNFa_BA.4.5.S1 Bcd8_TNFa_BA.4.5.S2 Bcd8_TNFa_COV2.CON.S1
##  Min.   :0.0010      Min.   :0.0010      Min.   : 0.0010      
##  1st Qu.:0.0048      1st Qu.:0.0010      1st Qu.: 0.0031      
##  Median :0.0304      Median :0.0083      Median : 0.0257      
##  Mean   :0.2273      Mean   :0.0478      Mean   : 0.2277      
##  3rd Qu.:0.1071      3rd Qu.:0.0318      3rd Qu.: 0.1144      
##  Max.   :9.0860      Max.   :1.8457      Max.   :10.0111      
##  NA's   :694         NA's   :710         NA's   :686          
##  Bcd8_TNFa_COV2.CON.S2 Bcd8_TNFa_Wuhan.N Day15cd4_154_BA.4.5.S1
##  Min.   :0.0010        Min.   :0.0010    Min.   :0.0010        
##  1st Qu.:0.0010        1st Qu.:0.0010    1st Qu.:0.0547        
##  Median :0.0074        Median :0.0010    Median :0.0879        
##  Mean   :0.0483        Mean   :0.0103    Mean   :0.1260        
##  3rd Qu.:0.0257        3rd Qu.:0.0080    3rd Qu.:0.1577        
##  Max.   :4.8425        Max.   :0.8312    Max.   :1.3949        
##  NA's   :686           NA's   :746       NA's   :693           
##  Day15cd4_154_BA.4.5.S2 Day15cd4_154_COV2.CON.S1 Day15cd4_154_COV2.CON.S2
##  Min.   :0.0010         Min.   :0.0079           Min.   :0.0041          
##  1st Qu.:0.0673         1st Qu.:0.0746           1st Qu.:0.0742          
##  Median :0.1124         Median :0.1185           Median :0.1290          
##  Mean   :0.1488         Mean   :0.1627           Mean   :0.1622          
##  3rd Qu.:0.1977         3rd Qu.:0.1953           3rd Qu.:0.2037          
##  Max.   :0.8099         Max.   :1.6033           Max.   :1.0294          
##  NA's   :703            NA's   :686              NA's   :686             
##  Day15cd4_154_Wuhan.N Day15cd4_CXCR5.154_BA.4.5.S1 Day15cd4_CXCR5.154_BA.4.5.S2
##  Min.   :0.0010       Min.   :0.0010               Min.   :0.0010              
##  1st Qu.:0.0018       1st Qu.:0.0023               1st Qu.:0.0028              
##  Median :0.0081       Median :0.0054               Median :0.0053              
##  Mean   :0.0176       Mean   :0.0088               Mean   :0.0090              
##  3rd Qu.:0.0204       3rd Qu.:0.0107               3rd Qu.:0.0102              
##  Max.   :0.4795       Max.   :0.1835               Max.   :0.4291              
##  NA's   :717          NA's   :701                  NA's   :706                 
##  Day15cd4_CXCR5.154_COV2.CON.S1 Day15cd4_CXCR5.154_COV2.CON.S2
##  Min.   :0.0010                 Min.   :0.0010                
##  1st Qu.:0.0045                 1st Qu.:0.0033                
##  Median :0.0089                 Median :0.0072                
##  Mean   :0.0132                 Mean   :0.0108                
##  3rd Qu.:0.0169                 3rd Qu.:0.0123                
##  Max.   :0.2213                 Max.   :0.4744                
##  NA's   :687                    NA's   :686                   
##  Day15cd4_CXCR5.154_Wuhan.N Day15cd4_CXCR5.IL21_BA.4.5.S1
##  Min.   :0.0010             Min.   :0.0010               
##  1st Qu.:0.0010             1st Qu.:0.0010               
##  Median :0.0010             Median :0.0011               
##  Mean   :0.0026             Mean   :0.0023               
##  3rd Qu.:0.0024             3rd Qu.:0.0026               
##  Max.   :0.0636             Max.   :0.0265               
##  NA's   :723                NA's   :701                  
##  Day15cd4_CXCR5.IL21_BA.4.5.S2 Day15cd4_CXCR5.IL21_COV2.CON.S1
##  Min.   :0.0010                Min.   :0.0010                 
##  1st Qu.:0.0010                1st Qu.:0.0010                 
##  Median :0.0012                Median :0.0020                 
##  Mean   :0.0023                Mean   :0.0036                 
##  3rd Qu.:0.0030                3rd Qu.:0.0047                 
##  Max.   :0.0150                Max.   :0.0321                 
##  NA's   :706                   NA's   :687                    
##  Day15cd4_CXCR5.IL21_COV2.CON.S2 Day15cd4_CXCR5.IL21_Wuhan.N
##  Min.   :0.0010                  Min.   :0.0010             
##  1st Qu.:0.0010                  1st Qu.:0.0010             
##  Median :0.0015                  Median :0.0010             
##  Mean   :0.0028                  Mean   :0.0013             
##  3rd Qu.:0.0035                  3rd Qu.:0.0010             
##  Max.   :0.0221                  Max.   :0.0217             
##  NA's   :686                     NA's   :723                
##  Day15cd4_IFNg_BA.4.5.S1 Day15cd4_IFNg_BA.4.5.S2 Day15cd4_IFNg_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0032          Min.   :0.0010           
##  1st Qu.:0.0378          1st Qu.:0.0518          1st Qu.:0.0529           
##  Median :0.0666          Median :0.0901          Median :0.0883           
##  Mean   :0.0927          Mean   :0.1182          Mean   :0.1199           
##  3rd Qu.:0.1126          3rd Qu.:0.1552          3rd Qu.:0.1436           
##  Max.   :1.0689          Max.   :0.7476          Max.   :1.1782           
##  NA's   :693             NA's   :703             NA's   :686              
##  Day15cd4_IFNg_COV2.CON.S2 Day15cd4_IFNg_Wuhan.N Day15cd4_IFNg.IL2_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010             
##  1st Qu.:0.0579            1st Qu.:0.0010        1st Qu.:0.0556             
##  Median :0.1000            Median :0.0044        Median :0.0941             
##  Mean   :0.1277            Mean   :0.0117        Mean   :0.1315             
##  3rd Qu.:0.1692            3rd Qu.:0.0131        3rd Qu.:0.1643             
##  Max.   :0.8221            Max.   :0.2068        Max.   :1.2915             
##  NA's   :686               NA's   :717           NA's   :693                
##  Day15cd4_IFNg.IL2_BA.4.5.S2 Day15cd4_IFNg.IL2_COV2.CON.S1
##  Min.   :0.0010              Min.   :0.0010               
##  1st Qu.:0.0723              1st Qu.:0.0778               
##  Median :0.1218              Median :0.1233               
##  Mean   :0.1610              Mean   :0.1700               
##  3rd Qu.:0.2120              3rd Qu.:0.2029               
##  Max.   :0.7926              Max.   :1.4200               
##  NA's   :703                 NA's   :686                  
##  Day15cd4_IFNg.IL2_COV2.CON.S2 Day15cd4_IFNg.IL2_Wuhan.N
##  Min.   :0.0010                Min.   :0.0010           
##  1st Qu.:0.0832                1st Qu.:0.0010           
##  Median :0.1386                Median :0.0055           
##  Mean   :0.1760                Mean   :0.0162           
##  3rd Qu.:0.2258                3rd Qu.:0.0190           
##  Max.   :0.9630                Max.   :0.4074           
##  NA's   :686                   NA's   :717              
##  Day15cd4_IFNg.IL2.154_BA.4.5.S1 Day15cd4_IFNg.IL2.154_BA.4.5.S2
##  Min.   :0.0010                  Min.   :0.0010                 
##  1st Qu.:0.0637                  1st Qu.:0.0803                 
##  Median :0.1046                  Median :0.1395                 
##  Mean   :0.1483                  Mean   :0.1778                 
##  3rd Qu.:0.1883                  3rd Qu.:0.2287                 
##  Max.   :1.4881                  Max.   :0.9375                 
##  NA's   :693                     NA's   :703                    
##  Day15cd4_IFNg.IL2.154_COV2.CON.S1 Day15cd4_IFNg.IL2.154_COV2.CON.S2
##  Min.   :0.0010                    Min.   :0.0010                   
##  1st Qu.:0.0861                    1st Qu.:0.0905                   
##  Median :0.1416                    Median :0.1524                   
##  Mean   :0.1907                    Mean   :0.1952                   
##  3rd Qu.:0.2285                    3rd Qu.:0.2491                   
##  Max.   :1.6908                    Max.   :1.1756                   
##  NA's   :686                       NA's   :686                      
##  Day15cd4_IFNg.IL2.154_Wuhan.N Day15cd4_IL17a_BA.4.5.S1
##  Min.   :0.0010                Min.   :0.0010          
##  1st Qu.:0.0010                1st Qu.:0.0010          
##  Median :0.0067                Median :0.0010          
##  Mean   :0.0187                Mean   :0.0017          
##  3rd Qu.:0.0224                3rd Qu.:0.0014          
##  Max.   :0.5227                Max.   :0.0139          
##  NA's   :717                   NA's   :693             
##  Day15cd4_IL17a_BA.4.5.S2 Day15cd4_IL17a_COV2.CON.S1 Day15cd4_IL17a_COV2.CON.S2
##  Min.   :0.0010           Min.   :0.0010             Min.   :0.0010            
##  1st Qu.:0.0010           1st Qu.:0.0010             1st Qu.:0.0010            
##  Median :0.0010           Median :0.0010             Median :0.0010            
##  Mean   :0.0017           Mean   :0.0019             Mean   :0.0018            
##  3rd Qu.:0.0017           3rd Qu.:0.0017             3rd Qu.:0.0017            
##  Max.   :0.0152           Max.   :0.0224             Max.   :0.0176            
##  NA's   :703              NA's   :686                NA's   :686               
##  Day15cd4_IL17a_Wuhan.N Day15cd4_IL2_BA.4.5.S1 Day15cd4_IL2_BA.4.5.S2
##  Min.   :0.0010         Min.   :0.0010         Min.   :0.0010        
##  1st Qu.:0.0010         1st Qu.:0.0335         1st Qu.:0.0415        
##  Median :0.0010         Median :0.0584         Median :0.0749        
##  Mean   :0.0013         Mean   :0.0894         Mean   :0.1057        
##  3rd Qu.:0.0010         3rd Qu.:0.1137         3rd Qu.:0.1363        
##  Max.   :0.0109         Max.   :0.8232         Max.   :0.6468        
##  NA's   :717            NA's   :693            NA's   :703           
##  Day15cd4_IL2_COV2.CON.S1 Day15cd4_IL2_COV2.CON.S2 Day15cd4_IL2_Wuhan.N
##  Min.   :0.0010           Min.   :0.0010           Min.   :0.0010      
##  1st Qu.:0.0450           1st Qu.:0.0497           1st Qu.:0.0010      
##  Median :0.0804           Median :0.0858           Median :0.0037      
##  Mean   :0.1162           Mean   :0.1180           Mean   :0.0128      
##  3rd Qu.:0.1366           3rd Qu.:0.1491           3rd Qu.:0.0150      
##  Max.   :0.9056           Max.   :0.7909           Max.   :0.3852      
##  NA's   :686              NA's   :686              NA's   :717         
##  Day15cd4_IL21_BA.4.5.S1 Day15cd4_IL21_BA.4.5.S2 Day15cd4_IL21_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0047          1st Qu.:0.0071          1st Qu.:0.0078           
##  Median :0.0126          Median :0.0159          Median :0.0171           
##  Mean   :0.0177          Mean   :0.0226          Mean   :0.0238           
##  3rd Qu.:0.0243          3rd Qu.:0.0300          3rd Qu.:0.0315           
##  Max.   :0.2645          Max.   :0.2539          Max.   :0.2822           
##  NA's   :693             NA's   :703             NA's   :686              
##  Day15cd4_IL21_COV2.CON.S2 Day15cd4_IL21_Wuhan.N Day15cd4_IL4.154_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010            
##  1st Qu.:0.0077            1st Qu.:0.0010        1st Qu.:0.0010            
##  Median :0.0177            Median :0.0010        Median :0.0010            
##  Mean   :0.0250            Mean   :0.0034        Mean   :0.0028            
##  3rd Qu.:0.0331            3rd Qu.:0.0039        3rd Qu.:0.0026            
##  Max.   :0.2899            Max.   :0.0630        Max.   :0.0353            
##  NA's   :686               NA's   :717           NA's   :693               
##  Day15cd4_IL4.154_BA.4.5.S2 Day15cd4_IL4.154_COV2.CON.S1
##  Min.   :0.0010             Min.   :0.0010              
##  1st Qu.:0.0010             1st Qu.:0.0010              
##  Median :0.0011             Median :0.0013              
##  Mean   :0.0029             Mean   :0.0037              
##  3rd Qu.:0.0028             3rd Qu.:0.0035              
##  Max.   :0.0530             Max.   :0.0607              
##  NA's   :703                NA's   :686                 
##  Day15cd4_IL4.154_COV2.CON.S2 Day15cd4_IL4.154_Wuhan.N
##  Min.   :0.0010               Min.   :0.0010          
##  1st Qu.:0.0010               1st Qu.:0.0010          
##  Median :0.0013               Median :0.0010          
##  Mean   :0.0033               Mean   :0.0011          
##  3rd Qu.:0.0033               3rd Qu.:0.0010          
##  Max.   :0.0569               Max.   :0.0073          
##  NA's   :686                  NA's   :717             
##  Day15cd4_IL4.IL5.IL13.154_BA.4.5.S1 Day15cd4_IL4.IL5.IL13.154_BA.4.5.S2
##  Min.   :0.0010                      Min.   :0.0010                     
##  1st Qu.:0.0010                      1st Qu.:0.0010                     
##  Median :0.0011                      Median :0.0013                     
##  Mean   :0.0033                      Mean   :0.0035                     
##  3rd Qu.:0.0032                      3rd Qu.:0.0034                     
##  Max.   :0.0522                      Max.   :0.0608                     
##  NA's   :693                         NA's   :703                        
##  Day15cd4_IL4.IL5.IL13.154_COV2.CON.S1 Day15cd4_IL4.IL5.IL13.154_COV2.CON.S2
##  Min.   :0.0010                        Min.   :0.0010                       
##  1st Qu.:0.0010                        1st Qu.:0.0010                       
##  Median :0.0015                        Median :0.0015                       
##  Mean   :0.0046                        Mean   :0.0039                       
##  3rd Qu.:0.0045                        3rd Qu.:0.0042                       
##  Max.   :0.0767                        Max.   :0.0599                       
##  NA's   :686                           NA's   :686                          
##  Day15cd4_IL4.IL5.IL13.154_Wuhan.N Day15cd4_IL5.IL13.154_BA.4.5.S1
##  Min.   :0.0010                    Min.   :0.0010                 
##  1st Qu.:0.0010                    1st Qu.:0.0010                 
##  Median :0.0010                    Median :0.0010                 
##  Mean   :0.0011                    Mean   :0.0020                 
##  3rd Qu.:0.0010                    3rd Qu.:0.0012                 
##  Max.   :0.0106                    Max.   :0.0364                 
##  NA's   :717                       NA's   :693                    
##  Day15cd4_IL5.IL13.154_BA.4.5.S2 Day15cd4_IL5.IL13.154_COV2.CON.S1
##  Min.   :0.0010                  Min.   :0.0010                   
##  1st Qu.:0.0010                  1st Qu.:0.0010                   
##  Median :0.0010                  Median :0.0010                   
##  Mean   :0.0020                  Mean   :0.0026                   
##  3rd Qu.:0.0014                  3rd Qu.:0.0017                   
##  Max.   :0.0412                  Max.   :0.0479                   
##  NA's   :703                     NA's   :686                      
##  Day15cd4_IL5.IL13.154_COV2.CON.S2 Day15cd4_IL5.IL13.154_Wuhan.N
##  Min.   :0.0010                    Min.   :0.0010               
##  1st Qu.:0.0010                    1st Qu.:0.0010               
##  Median :0.0010                    Median :0.0010               
##  Mean   :0.0020                    Mean   :0.0011               
##  3rd Qu.:0.0015                    3rd Qu.:0.0010               
##  Max.   :0.0358                    Max.   :0.0065               
##  NA's   :686                       NA's   :717                  
##  Day15cd4_TNFa_BA.4.5.S1 Day15cd4_TNFa_BA.4.5.S2 Day15cd4_TNFa_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0303          1st Qu.:0.0441          1st Qu.:0.0330           
##  Median :0.0734          Median :0.0960          Median :0.0914           
##  Mean   :0.1168          Mean   :0.1385          Mean   :0.1402           
##  3rd Qu.:0.1558          3rd Qu.:0.1863          3rd Qu.:0.1764           
##  Max.   :1.2295          Max.   :0.9793          Max.   :1.3111           
##  NA's   :693             NA's   :703             NA's   :686              
##  Day15cd4_TNFa_COV2.CON.S2 Day15cd4_TNFa_Wuhan.N Day15cd8_IFNg_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   : 0.0010        
##  1st Qu.:0.0458            1st Qu.:0.0010        1st Qu.: 0.0124        
##  Median :0.1059            Median :0.0010        Median : 0.0487        
##  Mean   :0.1522            Mean   :0.0093        Mean   : 0.5142        
##  3rd Qu.:0.2051            3rd Qu.:0.0061        3rd Qu.: 0.2704        
##  Max.   :1.2638            Max.   :0.5546        Max.   :16.5486        
##  NA's   :686               NA's   :717           NA's   :695            
##  Day15cd8_IFNg_BA.4.5.S2 Day15cd8_IFNg_COV2.CON.S1 Day15cd8_IFNg_COV2.CON.S2
##  Min.   :0.0010          Min.   : 0.0010           Min.   :0.0010           
##  1st Qu.:0.0029          1st Qu.: 0.0151           1st Qu.:0.0048           
##  Median :0.0171          Median : 0.0688           Median :0.0156           
##  Mean   :0.1062          Mean   : 0.5285           Mean   :0.1205           
##  3rd Qu.:0.0625          3rd Qu.: 0.3013           3rd Qu.:0.0510           
##  Max.   :9.2387          Max.   :16.0068           Max.   :8.7407           
##  NA's   :703             NA's   :687               NA's   :686              
##  Day15cd8_IFNg_Wuhan.N Day15cd8_IFNg.IL2_BA.4.5.S1 Day15cd8_IFNg.IL2_BA.4.5.S2
##  Min.   :0.0010        Min.   : 0.0010             Min.   :0.0010             
##  1st Qu.:0.0010        1st Qu.: 0.0119             1st Qu.:0.0030             
##  Median :0.0010        Median : 0.0495             Median :0.0166             
##  Mean   :0.0118        Mean   : 0.5150             Mean   :0.1063             
##  3rd Qu.:0.0066        3rd Qu.: 0.2752             3rd Qu.:0.0627             
##  Max.   :1.0833        Max.   :16.5524             Max.   :9.2387             
##  NA's   :719           NA's   :695                 NA's   :703                
##  Day15cd8_IFNg.IL2_COV2.CON.S1 Day15cd8_IFNg.IL2_COV2.CON.S2
##  Min.   : 0.0010               Min.   :0.0010               
##  1st Qu.: 0.0159               1st Qu.:0.0041               
##  Median : 0.0692               Median :0.0149               
##  Mean   : 0.5296               Mean   :0.1207               
##  3rd Qu.: 0.3030               3rd Qu.:0.0521               
##  Max.   :16.0073               Max.   :8.7407               
##  NA's   :687                   NA's   :686                  
##  Day15cd8_IFNg.IL2_Wuhan.N Day15cd8_IFNg.IL2.TNFa_BA.4.5.S1
##  Min.   :0.0010            Min.   : 0.0010                 
##  1st Qu.:0.0010            1st Qu.: 0.0132                 
##  Median :0.0010            Median : 0.0594                 
##  Mean   :0.0119            Mean   : 0.5256                 
##  3rd Qu.:0.0069            3rd Qu.: 0.2867                 
##  Max.   :1.0833            Max.   :16.5758                 
##  NA's   :719               NA's   :695                     
##  Day15cd8_IFNg.IL2.TNFa_BA.4.5.S2 Day15cd8_IFNg.IL2.TNFa_COV2.CON.S1
##  Min.   :0.0010                   Min.   : 0.0010                   
##  1st Qu.:0.0010                   1st Qu.: 0.0140                   
##  Median :0.0193                   Median : 0.0682                   
##  Mean   :0.1134                   Mean   : 0.5381                   
##  3rd Qu.:0.0709                   3rd Qu.: 0.3210                   
##  Max.   :9.2822                   Max.   :16.0581                   
##  NA's   :703                      NA's   :687                       
##  Day15cd8_IFNg.IL2.TNFa_COV2.CON.S2 Day15cd8_IFNg.IL2.TNFa_Wuhan.N
##  Min.   :0.0010                     Min.   :0.0010                
##  1st Qu.:0.0019                     1st Qu.:0.0010                
##  Median :0.0184                     Median :0.0010                
##  Mean   :0.1254                     Mean   :0.0132                
##  3rd Qu.:0.0638                     3rd Qu.:0.0088                
##  Max.   :8.9171                     Max.   :1.0908                
##  NA's   :686                        NA's   :719                   
##  Day15cd8_IL2_BA.4.5.S1 Day15cd8_IL2_BA.4.5.S2 Day15cd8_IL2_COV2.CON.S1
##  Min.   :0.0010         Min.   :0.0010         Min.   :0.0010          
##  1st Qu.:0.0010         1st Qu.:0.0010         1st Qu.:0.0010          
##  Median :0.0063         Median :0.0020         Median :0.0076          
##  Mean   :0.0398         Mean   :0.0088         Mean   :0.0356          
##  3rd Qu.:0.0302         3rd Qu.:0.0065         3rd Qu.:0.0282          
##  Max.   :2.2593         Max.   :0.2397         Max.   :2.2919          
##  NA's   :695            NA's   :703            NA's   :687             
##  Day15cd8_IL2_COV2.CON.S2 Day15cd8_IL2_Wuhan.N Day15cd8_TNFa_BA.4.5.S1
##  Min.   :0.0010           Min.   :0.0010       Min.   : 0.0010        
##  1st Qu.:0.0010           1st Qu.:0.0010       1st Qu.: 0.0063        
##  Median :0.0025           Median :0.0010       Median : 0.0319        
##  Mean   :0.0104           Mean   :0.0043       Mean   : 0.3178        
##  3rd Qu.:0.0076           3rd Qu.:0.0025       3rd Qu.: 0.1581        
##  Max.   :0.4038           Max.   :0.3199       Max.   :15.0926        
##  NA's   :686              NA's   :719          NA's   :695            
##  Day15cd8_TNFa_BA.4.5.S2 Day15cd8_TNFa_COV2.CON.S1 Day15cd8_TNFa_COV2.CON.S2
##  Min.   :0.0010          Min.   : 0.0010           Min.   :0.0010           
##  1st Qu.:0.0010          1st Qu.: 0.0045           1st Qu.:0.0010           
##  Median :0.0107          Median : 0.0300           Median :0.0085           
##  Mean   :0.0640          Mean   : 0.2965           Mean   :0.0725           
##  3rd Qu.:0.0409          3rd Qu.: 0.1721           3rd Qu.:0.0380           
##  Max.   :2.0666          Max.   :14.7401           Max.   :7.4199           
##  NA's   :703             NA's   :687               NA's   :686              
##  Day15cd8_TNFa_Wuhan.N Day91cd4_154_BA.4.5.S1 Day91cd4_154_BA.4.5.S2
##  Min.   :0.0010        Min.   :0.0010         Min.   :0.0010        
##  1st Qu.:0.0010        1st Qu.:0.0256         1st Qu.:0.0361        
##  Median :0.0010        Median :0.0472         Median :0.0635        
##  Mean   :0.0087        Mean   :0.0660         Mean   :0.0787        
##  3rd Qu.:0.0064        3rd Qu.:0.0854         3rd Qu.:0.1006        
##  Max.   :0.9568        Max.   :0.3996         Max.   :0.4515        
##  NA's   :719           NA's   :1092           NA's   :1094          
##  Day91cd4_154_COV2.CON.S1 Day91cd4_154_COV2.CON.S2 Day91cd4_154_Wuhan.N
##  Min.   :0.0042           Min.   :0.0010           Min.   :0.0010      
##  1st Qu.:0.0407           1st Qu.:0.0418           1st Qu.:0.0038      
##  Median :0.0659           Median :0.0703           Median :0.0118      
##  Mean   :0.0873           Mean   :0.0886           Mean   :0.0179      
##  3rd Qu.:0.1056           3rd Qu.:0.1099           3rd Qu.:0.0260      
##  Max.   :0.5735           Max.   :0.6552           Max.   :0.1041      
##  NA's   :1088             NA's   :1088             NA's   :1105        
##  Day91cd4_CXCR5.154_BA.4.5.S1 Day91cd4_CXCR5.154_BA.4.5.S2
##  Min.   :0.0010               Min.   :0.0010              
##  1st Qu.:0.0012               1st Qu.:0.0010              
##  Median :0.0031               Median :0.0021              
##  Mean   :0.0045               Mean   :0.0037              
##  3rd Qu.:0.0061               3rd Qu.:0.0050              
##  Max.   :0.0265               Max.   :0.0279              
##  NA's   :1099                 NA's   :1096                
##  Day91cd4_CXCR5.154_COV2.CON.S1 Day91cd4_CXCR5.154_COV2.CON.S2
##  Min.   :0.0010                 Min.   :0.0010                
##  1st Qu.:0.0017                 1st Qu.:0.0010                
##  Median :0.0036                 Median :0.0031                
##  Mean   :0.0053                 Mean   :0.0044                
##  3rd Qu.:0.0066                 3rd Qu.:0.0059                
##  Max.   :0.0404                 Max.   :0.0345                
##  NA's   :1088                   NA's   :1088                  
##  Day91cd4_CXCR5.154_Wuhan.N Day91cd4_CXCR5.IL21_BA.4.5.S1
##  Min.   :0.0010             Min.   :0.0010               
##  1st Qu.:0.0010             1st Qu.:0.0010               
##  Median :0.0013             Median :0.0010               
##  Mean   :0.0032             Mean   :0.0019               
##  3rd Qu.:0.0041             3rd Qu.:0.0024               
##  Max.   :0.0195             Max.   :0.0097               
##  NA's   :1111               NA's   :1099                 
##  Day91cd4_CXCR5.IL21_BA.4.5.S2 Day91cd4_CXCR5.IL21_COV2.CON.S1
##  Min.   :0.0010                Min.   :0.0010                 
##  1st Qu.:0.0010                1st Qu.:0.0010                 
##  Median :0.0010                Median :0.0012                 
##  Mean   :0.0018                Mean   :0.0021                 
##  3rd Qu.:0.0020                3rd Qu.:0.0026                 
##  Max.   :0.0143                Max.   :0.0112                 
##  NA's   :1096                  NA's   :1088                   
##  Day91cd4_CXCR5.IL21_COV2.CON.S2 Day91cd4_CXCR5.IL21_Wuhan.N
##  Min.   :0.0010                  Min.   :0.0010             
##  1st Qu.:0.0010                  1st Qu.:0.0010             
##  Median :0.0010                  Median :0.0010             
##  Mean   :0.0020                  Mean   :0.0013             
##  3rd Qu.:0.0023                  3rd Qu.:0.0013             
##  Max.   :0.0093                  Max.   :0.0042             
##  NA's   :1088                    NA's   :1111               
##  Day91cd4_IFNg_BA.4.5.S1 Day91cd4_IFNg_BA.4.5.S2 Day91cd4_IFNg_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0030          Min.   :0.0010           
##  1st Qu.:0.0221          1st Qu.:0.0303          1st Qu.:0.0314           
##  Median :0.0377          Median :0.0527          Median :0.0507           
##  Mean   :0.0490          Mean   :0.0641          Mean   :0.0629           
##  3rd Qu.:0.0657          3rd Qu.:0.0823          3rd Qu.:0.0794           
##  Max.   :0.2286          Max.   :0.3369          Max.   :0.3156           
##  NA's   :1092            NA's   :1094            NA's   :1088             
##  Day91cd4_IFNg_COV2.CON.S2 Day91cd4_IFNg_Wuhan.N Day91cd4_IFNg.IL2_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010             
##  1st Qu.:0.0370            1st Qu.:0.0011        1st Qu.:0.0320             
##  Median :0.0614            Median :0.0076        Median :0.0602             
##  Mean   :0.0706            Mean   :0.0137        Mean   :0.0817             
##  3rd Qu.:0.0933            3rd Qu.:0.0195        3rd Qu.:0.0918             
##  Max.   :0.3189            Max.   :0.0954        Max.   :0.5515             
##  NA's   :1088              NA's   :1105          NA's   :1092               
##  Day91cd4_IFNg.IL2_BA.4.5.S2 Day91cd4_IFNg.IL2_COV2.CON.S1
##  Min.   :0.0010              Min.   :0.0010               
##  1st Qu.:0.0442              1st Qu.:0.0456               
##  Median :0.0702              Median :0.0775               
##  Mean   :0.0979              Mean   :0.1031               
##  3rd Qu.:0.1218              3rd Qu.:0.1192               
##  Max.   :0.7309              Max.   :0.7888               
##  NA's   :1094                NA's   :1088                 
##  Day91cd4_IFNg.IL2_COV2.CON.S2 Day91cd4_IFNg.IL2_Wuhan.N
##  Min.   :0.0019                Min.   :0.0010           
##  1st Qu.:0.0501                1st Qu.:0.0010           
##  Median :0.0853                Median :0.0114           
##  Mean   :0.1100                Mean   :0.0208           
##  3rd Qu.:0.1368                3rd Qu.:0.0285           
##  Max.   :0.7924                Max.   :0.1231           
##  NA's   :1088                  NA's   :1105             
##  Day91cd4_IFNg.IL2.154_BA.4.5.S1 Day91cd4_IFNg.IL2.154_BA.4.5.S2
##  Min.   :0.0010                  Min.   :0.0010                 
##  1st Qu.:0.0353                  1st Qu.:0.0455                 
##  Median :0.0662                  Median :0.0801                 
##  Mean   :0.0887                  Mean   :0.1048                 
##  3rd Qu.:0.1017                  3rd Qu.:0.1291                 
##  Max.   :0.5840                  Max.   :0.7868                 
##  NA's   :1092                    NA's   :1094                   
##  Day91cd4_IFNg.IL2.154_COV2.CON.S1 Day91cd4_IFNg.IL2.154_COV2.CON.S2
##  Min.   :0.0010                    Min.   :0.0027                   
##  1st Qu.:0.0480                    1st Qu.:0.0518                   
##  Median :0.0863                    Median :0.0919                   
##  Mean   :0.1128                    Mean   :0.1185                   
##  3rd Qu.:0.1330                    3rd Qu.:0.1440                   
##  Max.   :0.8670                    Max.   :0.8962                   
##  NA's   :1088                      NA's   :1088                     
##  Day91cd4_IFNg.IL2.154_Wuhan.N Day91cd4_IL17a_BA.4.5.S1
##  Min.   :0.0010                Min.   :0.0010          
##  1st Qu.:0.0014                1st Qu.:0.0010          
##  Median :0.0146                Median :0.0010          
##  Mean   :0.0226                Mean   :0.0014          
##  3rd Qu.:0.0309                3rd Qu.:0.0011          
##  Max.   :0.1292                Max.   :0.0101          
##  NA's   :1105                  NA's   :1092            
##  Day91cd4_IL17a_BA.4.5.S2 Day91cd4_IL17a_COV2.CON.S1 Day91cd4_IL17a_COV2.CON.S2
##  Min.   :0.0010           Min.   :0.0010             Min.   :0.0010            
##  1st Qu.:0.0010           1st Qu.:0.0010             1st Qu.:0.0010            
##  Median :0.0010           Median :0.0010             Median :0.0010            
##  Mean   :0.0014           Mean   :0.0014             Mean   :0.0014            
##  3rd Qu.:0.0012           3rd Qu.:0.0011             3rd Qu.:0.0012            
##  Max.   :0.0082           Max.   :0.0082             Max.   :0.0076            
##  NA's   :1094             NA's   :1088               NA's   :1088              
##  Day91cd4_IL17a_Wuhan.N Day91cd4_IL2_BA.4.5.S1 Day91cd4_IL2_BA.4.5.S2
##  Min.   :0.0010         Min.   :0.0010         Min.   :0.0010        
##  1st Qu.:0.0010         1st Qu.:0.0207         1st Qu.:0.0285        
##  Median :0.0010         Median :0.0431         Median :0.0492        
##  Mean   :0.0012         Mean   :0.0657         Mean   :0.0745        
##  3rd Qu.:0.0010         3rd Qu.:0.0724         3rd Qu.:0.0918        
##  Max.   :0.0052         Max.   :0.5320         Max.   :0.6896        
##  NA's   :1105           NA's   :1092           NA's   :1094          
##  Day91cd4_IL2_COV2.CON.S1 Day91cd4_IL2_COV2.CON.S2 Day91cd4_IL2_Wuhan.N
##  Min.   :0.0010           Min.   :0.0010           Min.   :0.0010      
##  1st Qu.:0.0285           1st Qu.:0.0327           1st Qu.:0.0015      
##  Median :0.0587           Median :0.0571           Median :0.0091      
##  Mean   :0.0828           Mean   :0.0850           Mean   :0.0172      
##  3rd Qu.:0.0944           3rd Qu.:0.1048           3rd Qu.:0.0227      
##  Max.   :0.7441           Max.   :0.7521           Max.   :0.1147      
##  NA's   :1088             NA's   :1088             NA's   :1105        
##  Day91cd4_IL21_BA.4.5.S1 Day91cd4_IL21_BA.4.5.S2 Day91cd4_IL21_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0010          1st Qu.:0.0010          1st Qu.:0.0010           
##  Median :0.0034          Median :0.0038          Median :0.0048           
##  Mean   :0.0063          Mean   :0.0065          Mean   :0.0073           
##  3rd Qu.:0.0089          3rd Qu.:0.0095          3rd Qu.:0.0100           
##  Max.   :0.0446          Max.   :0.0579          Max.   :0.0534           
##  NA's   :1092            NA's   :1094            NA's   :1088             
##  Day91cd4_IL21_COV2.CON.S2 Day91cd4_IL21_Wuhan.N Day91cd4_IL4.154_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010            
##  1st Qu.:0.0010            1st Qu.:0.0010        1st Qu.:0.0010            
##  Median :0.0035            Median :0.0010        Median :0.0010            
##  Mean   :0.0070            Mean   :0.0030        Mean   :0.0017            
##  3rd Qu.:0.0097            3rd Qu.:0.0039        3rd Qu.:0.0010            
##  Max.   :0.0529            Max.   :0.0176        Max.   :0.0357            
##  NA's   :1088              NA's   :1105          NA's   :1092              
##  Day91cd4_IL4.154_BA.4.5.S2 Day91cd4_IL4.154_COV2.CON.S1
##  Min.   :0.0010             Min.   :0.0010              
##  1st Qu.:0.0010             1st Qu.:0.0010              
##  Median :0.0010             Median :0.0010              
##  Mean   :0.0016             Mean   :0.0018              
##  3rd Qu.:0.0011             3rd Qu.:0.0012              
##  Max.   :0.0169             Max.   :0.0270              
##  NA's   :1094               NA's   :1088                
##  Day91cd4_IL4.154_COV2.CON.S2 Day91cd4_IL4.154_Wuhan.N
##  Min.   :0.0010               Min.   :0.0010          
##  1st Qu.:0.0010               1st Qu.:0.0010          
##  Median :0.0010               Median :0.0010          
##  Mean   :0.0017               Mean   :0.0010          
##  3rd Qu.:0.0014               3rd Qu.:0.0010          
##  Max.   :0.0184               Max.   :0.0025          
##  NA's   :1088                 NA's   :1105            
##  Day91cd4_IL4.IL5.IL13.154_BA.4.5.S1 Day91cd4_IL4.IL5.IL13.154_BA.4.5.S2
##  Min.   :0.0010                      Min.   :0.0010                     
##  1st Qu.:0.0010                      1st Qu.:0.0010                     
##  Median :0.0010                      Median :0.0010                     
##  Mean   :0.0020                      Mean   :0.0018                     
##  3rd Qu.:0.0012                      3rd Qu.:0.0014                     
##  Max.   :0.0475                      Max.   :0.0219                     
##  NA's   :1092                        NA's   :1094                       
##  Day91cd4_IL4.IL5.IL13.154_COV2.CON.S1 Day91cd4_IL4.IL5.IL13.154_COV2.CON.S2
##  Min.   :0.0010                        Min.   :0.0010                       
##  1st Qu.:0.0010                        1st Qu.:0.0010                       
##  Median :0.0010                        Median :0.0010                       
##  Mean   :0.0023                        Mean   :0.0020                       
##  3rd Qu.:0.0013                        3rd Qu.:0.0016                       
##  Max.   :0.0369                        Max.   :0.0284                       
##  NA's   :1088                          NA's   :1088                         
##  Day91cd4_IL4.IL5.IL13.154_Wuhan.N Day91cd4_IL5.IL13.154_BA.4.5.S1
##  Min.   :0.0010                    Min.   :0.0010                 
##  1st Qu.:0.0010                    1st Qu.:0.0010                 
##  Median :0.0010                    Median :0.0010                 
##  Mean   :0.0011                    Mean   :0.0016                 
##  3rd Qu.:0.0010                    3rd Qu.:0.0010                 
##  Max.   :0.0033                    Max.   :0.0329                 
##  NA's   :1105                      NA's   :1092                   
##  Day91cd4_IL5.IL13.154_BA.4.5.S2 Day91cd4_IL5.IL13.154_COV2.CON.S1
##  Min.   :0.0010                  Min.   :0.0010                   
##  1st Qu.:0.0010                  1st Qu.:0.0010                   
##  Median :0.0010                  Median :0.0010                   
##  Mean   :0.0013                  Mean   :0.0017                   
##  3rd Qu.:0.0010                  3rd Qu.:0.0010                   
##  Max.   :0.0152                  Max.   :0.0227                   
##  NA's   :1094                    NA's   :1088                     
##  Day91cd4_IL5.IL13.154_COV2.CON.S2 Day91cd4_IL5.IL13.154_Wuhan.N
##  Min.   :0.0010                    Min.   :0.0010               
##  1st Qu.:0.0010                    1st Qu.:0.0010               
##  Median :0.0010                    Median :0.0010               
##  Mean   :0.0015                    Mean   :0.0011               
##  3rd Qu.:0.0010                    3rd Qu.:0.0010               
##  Max.   :0.0184                    Max.   :0.0033               
##  NA's   :1088                      NA's   :1105                 
##  Day91cd4_TNFa_BA.4.5.S1 Day91cd4_TNFa_BA.4.5.S2 Day91cd4_TNFa_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0222          1st Qu.:0.0260          1st Qu.:0.0165           
##  Median :0.0479          Median :0.0648          Median :0.0605           
##  Mean   :0.0764          Mean   :0.0907          Mean   :0.0894           
##  3rd Qu.:0.0852          3rd Qu.:0.1089          3rd Qu.:0.1055           
##  Max.   :0.6854          Max.   :0.9192          Max.   :0.9451           
##  NA's   :1092            NA's   :1094            NA's   :1088             
##  Day91cd4_TNFa_COV2.CON.S2 Day91cd4_TNFa_Wuhan.N Day91cd8_IFNg_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   : 0.0010        
##  1st Qu.:0.0252            1st Qu.:0.0010        1st Qu.: 0.0083        
##  Median :0.0664            Median :0.0010        Median : 0.0605        
##  Mean   :0.0994            Mean   :0.0100        Mean   : 0.5581        
##  3rd Qu.:0.1222            3rd Qu.:0.0116        3rd Qu.: 0.2957        
##  Max.   :0.9957            Max.   :0.1281        Max.   :14.2081        
##  NA's   :1088              NA's   :1105          NA's   :1093           
##  Day91cd8_IFNg_BA.4.5.S2 Day91cd8_IFNg_COV2.CON.S1 Day91cd8_IFNg_COV2.CON.S2
##  Min.   :0.0010          Min.   : 0.0010           Min.   :0.0010           
##  1st Qu.:0.0027          1st Qu.: 0.0124           1st Qu.:0.0035           
##  Median :0.0114          Median : 0.0749           Median :0.0138           
##  Mean   :0.0726          Mean   : 0.5225           Mean   :0.0780           
##  3rd Qu.:0.0510          3rd Qu.: 0.3535           3rd Qu.:0.0437           
##  Max.   :1.6579          Max.   :10.6086           Max.   :2.2747           
##  NA's   :1094            NA's   :1088              NA's   :1088             
##  Day91cd8_IFNg_Wuhan.N Day91cd8_IFNg.IL2_BA.4.5.S1 Day91cd8_IFNg.IL2_BA.4.5.S2
##  Min.   :0.0010        Min.   : 0.0010             Min.   :0.0010             
##  1st Qu.:0.0010        1st Qu.: 0.0096             1st Qu.:0.0023             
##  Median :0.0016        Median : 0.0605             Median :0.0119             
##  Mean   :0.0110        Mean   : 0.5601             Mean   :0.0728             
##  3rd Qu.:0.0107        3rd Qu.: 0.3005             3rd Qu.:0.0509             
##  Max.   :0.1907        Max.   :14.2104             Max.   :1.6582             
##  NA's   :1105          NA's   :1093                NA's   :1094               
##  Day91cd8_IFNg.IL2_COV2.CON.S1 Day91cd8_IFNg.IL2_COV2.CON.S2
##  Min.   : 0.0010               Min.   :0.0010               
##  1st Qu.: 0.0136               1st Qu.:0.0027               
##  Median : 0.0749               Median :0.0146               
##  Mean   : 0.5241               Mean   :0.0783               
##  3rd Qu.: 0.3610               3rd Qu.:0.0439               
##  Max.   :10.6086               Max.   :2.2722               
##  NA's   :1088                  NA's   :1088                 
##  Day91cd8_IFNg.IL2_Wuhan.N Day91cd8_IFNg.IL2.TNFa_BA.4.5.S1
##  Min.   :0.0010            Min.   : 0.0010                 
##  1st Qu.:0.0010            1st Qu.: 0.0196                 
##  Median :0.0025            Median : 0.0759                 
##  Mean   :0.0112            Mean   : 0.5779                 
##  3rd Qu.:0.0122            3rd Qu.: 0.3197                 
##  Max.   :0.2010            Max.   :14.3705                 
##  NA's   :1105              NA's   :1093                    
##  Day91cd8_IFNg.IL2.TNFa_BA.4.5.S2 Day91cd8_IFNg.IL2.TNFa_COV2.CON.S1
##  Min.   :0.0010                   Min.   : 0.0010                   
##  1st Qu.:0.0039                   1st Qu.: 0.0184                   
##  Median :0.0162                   Median : 0.0876                   
##  Mean   :0.0801                   Mean   : 0.5433                   
##  3rd Qu.:0.0534                   3rd Qu.: 0.3683                   
##  Max.   :1.6615                   Max.   :10.9200                   
##  NA's   :1094                     NA's   :1088                      
##  Day91cd8_IFNg.IL2.TNFa_COV2.CON.S2 Day91cd8_IFNg.IL2.TNFa_Wuhan.N
##  Min.   :0.0010                     Min.   :0.0010                
##  1st Qu.:0.0057                     1st Qu.:0.0010                
##  Median :0.0190                     Median :0.0019                
##  Mean   :0.0828                     Mean   :0.0126                
##  3rd Qu.:0.0503                     3rd Qu.:0.0142                
##  Max.   :2.2698                     Max.   :0.1967                
##  NA's   :1088                       NA's   :1105                  
##  Day91cd8_IL2_BA.4.5.S1 Day91cd8_IL2_BA.4.5.S2 Day91cd8_IL2_COV2.CON.S1
##  Min.   :0.0010         Min.   :0.0010         Min.   :0.0010          
##  1st Qu.:0.0010         1st Qu.:0.0010         1st Qu.:0.0028          
##  Median :0.0094         Median :0.0025         Median :0.0099          
##  Mean   :0.0448         Mean   :0.0069         Mean   :0.0347          
##  3rd Qu.:0.0351         3rd Qu.:0.0073         3rd Qu.:0.0332          
##  Max.   :0.9965         Max.   :0.1063         Max.   :0.4415          
##  NA's   :1093           NA's   :1094           NA's   :1088            
##  Day91cd8_IL2_COV2.CON.S2 Day91cd8_IL2_Wuhan.N Day91cd8_TNFa_BA.4.5.S1
##  Min.   :0.0010           Min.   :0.0010       Min.   : 0.0010        
##  1st Qu.:0.0010           1st Qu.:0.0010       1st Qu.: 0.0142        
##  Median :0.0028           Median :0.0010       Median : 0.0528        
##  Mean   :0.0073           Mean   :0.0046       Mean   : 0.4522        
##  3rd Qu.:0.0080           3rd Qu.:0.0036       3rd Qu.: 0.2355        
##  Max.   :0.0913           Max.   :0.0954       Max.   :11.7346        
##  NA's   :1088             NA's   :1105         NA's   :1093           
##  Day91cd8_TNFa_BA.4.5.S2 Day91cd8_TNFa_COV2.CON.S1 Day91cd8_TNFa_COV2.CON.S2
##  Min.   :0.0010          Min.   :0.0010            Min.   :0.0010           
##  1st Qu.:0.0010          1st Qu.:0.0079            1st Qu.:0.0010           
##  Median :0.0112          Median :0.0527            Median :0.0122           
##  Mean   :0.0588          Mean   :0.3995            Mean   :0.0610           
##  3rd Qu.:0.0378          3rd Qu.:0.2374            3rd Qu.:0.0364           
##  Max.   :1.0431          Max.   :7.2473            Max.   :1.6538           
##  NA's   :1094            NA's   :1088              NA's   :1088             
##  Day91cd8_TNFa_Wuhan.N Day181cd4_154_BA.4.5.S1 Day181cd4_154_BA.4.5.S2
##  Min.   :0.0010        Min.   :0.0010          Min.   :0.0066         
##  1st Qu.:0.0010        1st Qu.:0.0266          1st Qu.:0.0356         
##  Median :0.0010        Median :0.0466          Median :0.0542         
##  Mean   :0.0068        Mean   :0.0674          Mean   :0.0780         
##  3rd Qu.:0.0056        3rd Qu.:0.0786          3rd Qu.:0.0855         
##  Max.   :0.1183        Max.   :0.3538          Max.   :0.4304         
##  NA's   :1105          NA's   :1128            NA's   :1131           
##  Day181cd4_154_COV2.CON.S1 Day181cd4_154_COV2.CON.S2 Day181cd4_154_Wuhan.N
##  Min.   :0.0010            Min.   :0.0010            Min.   :0.0010       
##  1st Qu.:0.0363            1st Qu.:0.0382            1st Qu.:0.0038       
##  Median :0.0574            Median :0.0629            Median :0.0089       
##  Mean   :0.0860            Mean   :0.0895            Mean   :0.0172       
##  3rd Qu.:0.0970            3rd Qu.:0.1096            3rd Qu.:0.0215       
##  Max.   :0.4956            Max.   :0.5473            Max.   :0.0934       
##  NA's   :1123              NA's   :1123              NA's   :1137         
##  Day181cd4_CXCR5.154_BA.4.5.S1 Day181cd4_CXCR5.154_BA.4.5.S2
##  Min.   :0.0010                Min.   :0.0010               
##  1st Qu.:0.0010                1st Qu.:0.0010               
##  Median :0.0025                Median :0.0018               
##  Mean   :0.0034                Mean   :0.0031               
##  3rd Qu.:0.0048                3rd Qu.:0.0043               
##  Max.   :0.0174                Max.   :0.0154               
##  NA's   :1128                  NA's   :1131                 
##  Day181cd4_CXCR5.154_COV2.CON.S1 Day181cd4_CXCR5.154_COV2.CON.S2
##  Min.   :0.0010                  Min.   :0.0010                 
##  1st Qu.:0.0015                  1st Qu.:0.0010                 
##  Median :0.0034                  Median :0.0023                 
##  Mean   :0.0043                  Mean   :0.0035                 
##  3rd Qu.:0.0054                  3rd Qu.:0.0053                 
##  Max.   :0.0173                  Max.   :0.0203                 
##  NA's   :1123                    NA's   :1123                   
##  Day181cd4_CXCR5.154_Wuhan.N Day181cd4_CXCR5.IL21_BA.4.5.S1
##  Min.   :0.0010              Min.   :0.0010                
##  1st Qu.:0.0010              1st Qu.:0.0010                
##  Median :0.0013              Median :0.0010                
##  Mean   :0.0023              Mean   :0.0020                
##  3rd Qu.:0.0026              3rd Qu.:0.0023                
##  Max.   :0.0136              Max.   :0.0081                
##  NA's   :1143                NA's   :1128                  
##  Day181cd4_CXCR5.IL21_BA.4.5.S2 Day181cd4_CXCR5.IL21_COV2.CON.S1
##  Min.   :0.0010                 Min.   :0.0010                  
##  1st Qu.:0.0010                 1st Qu.:0.0010                  
##  Median :0.0010                 Median :0.0011                  
##  Mean   :0.0017                 Mean   :0.0023                  
##  3rd Qu.:0.0018                 3rd Qu.:0.0032                  
##  Max.   :0.0075                 Max.   :0.0130                  
##  NA's   :1131                   NA's   :1123                    
##  Day181cd4_CXCR5.IL21_COV2.CON.S2 Day181cd4_CXCR5.IL21_Wuhan.N
##  Min.   :0.0010                   Min.   :0.0010              
##  1st Qu.:0.0010                   1st Qu.:0.0010              
##  Median :0.0010                   Median :0.0010              
##  Mean   :0.0018                   Mean   :0.0013              
##  3rd Qu.:0.0021                   3rd Qu.:0.0012              
##  Max.   :0.0090                   Max.   :0.0060              
##  NA's   :1123                     NA's   :1143                
##  Day181cd4_IFNg_BA.4.5.S1 Day181cd4_IFNg_BA.4.5.S2 Day181cd4_IFNg_COV2.CON.S1
##  Min.   :0.0010           Min.   :0.0010           Min.   :0.0010            
##  1st Qu.:0.0212           1st Qu.:0.0282           1st Qu.:0.0300            
##  Median :0.0347           Median :0.0491           Median :0.0481            
##  Mean   :0.0509           Mean   :0.0649           Mean   :0.0643            
##  3rd Qu.:0.0651           3rd Qu.:0.0802           3rd Qu.:0.0795            
##  Max.   :0.2589           Max.   :0.3036           Max.   :0.3141            
##  NA's   :1128             NA's   :1131             NA's   :1123              
##  Day181cd4_IFNg_COV2.CON.S2 Day181cd4_IFNg_Wuhan.N Day181cd4_IFNg.IL2_BA.4.5.S1
##  Min.   :0.0010             Min.   :0.0010         Min.   :0.0010              
##  1st Qu.:0.0328             1st Qu.:0.0010         1st Qu.:0.0264              
##  Median :0.0553             Median :0.0064         Median :0.0540              
##  Mean   :0.0715             Mean   :0.0152         Mean   :0.0861              
##  3rd Qu.:0.0877             3rd Qu.:0.0178         3rd Qu.:0.1103              
##  Max.   :0.3479             Max.   :0.1464         Max.   :0.5222              
##  NA's   :1123               NA's   :1137           NA's   :1128                
##  Day181cd4_IFNg.IL2_BA.4.5.S2 Day181cd4_IFNg.IL2_COV2.CON.S1
##  Min.   :0.0010               Min.   :0.0010                
##  1st Qu.:0.0419               1st Qu.:0.0424                
##  Median :0.0761               Median :0.0721                
##  Mean   :0.0966               Mean   :0.1043                
##  3rd Qu.:0.1184               3rd Qu.:0.1115                
##  Max.   :0.5481               Max.   :0.6034                
##  NA's   :1131                 NA's   :1123                  
##  Day181cd4_IFNg.IL2_COV2.CON.S2 Day181cd4_IFNg.IL2_Wuhan.N
##  Min.   :0.0010                 Min.   :0.0010            
##  1st Qu.:0.0447                 1st Qu.:0.0010            
##  Median :0.0838                 Median :0.0059            
##  Mean   :0.1105                 Mean   :0.0213            
##  3rd Qu.:0.1349                 3rd Qu.:0.0290            
##  Max.   :0.6278                 Max.   :0.1394            
##  NA's   :1123                   NA's   :1137              
##  Day181cd4_IFNg.IL2.154_BA.4.5.S1 Day181cd4_IFNg.IL2.154_BA.4.5.S2
##  Min.   :0.0010                   Min.   :0.0010                  
##  1st Qu.:0.0291                   1st Qu.:0.0431                  
##  Median :0.0598                   Median :0.0779                  
##  Mean   :0.0926                   Mean   :0.1034                  
##  3rd Qu.:0.1147                   3rd Qu.:0.1250                  
##  Max.   :0.5409                   Max.   :0.6045                  
##  NA's   :1128                     NA's   :1131                    
##  Day181cd4_IFNg.IL2.154_COV2.CON.S1 Day181cd4_IFNg.IL2.154_COV2.CON.S2
##  Min.   :0.0010                     Min.   :0.0010                    
##  1st Qu.:0.0436                     1st Qu.:0.0467                    
##  Median :0.0786                     Median :0.0901                    
##  Mean   :0.1126                     Mean   :0.1180                    
##  3rd Qu.:0.1240                     3rd Qu.:0.1480                    
##  Max.   :0.6680                     Max.   :0.7136                    
##  NA's   :1123                       NA's   :1123                      
##  Day181cd4_IFNg.IL2.154_Wuhan.N Day181cd4_IL17a_BA.4.5.S1
##  Min.   :0.0010                 Min.   :0.0010           
##  1st Qu.:0.0010                 1st Qu.:0.0010           
##  Median :0.0081                 Median :0.0010           
##  Mean   :0.0224                 Mean   :0.0013           
##  3rd Qu.:0.0284                 3rd Qu.:0.0010           
##  Max.   :0.1441                 Max.   :0.0077           
##  NA's   :1137                   NA's   :1128             
##  Day181cd4_IL17a_BA.4.5.S2 Day181cd4_IL17a_COV2.CON.S1
##  Min.   :0.0010            Min.   :0.0010             
##  1st Qu.:0.0010            1st Qu.:0.0010             
##  Median :0.0010            Median :0.0010             
##  Mean   :0.0014            Mean   :0.0013             
##  3rd Qu.:0.0010            3rd Qu.:0.0010             
##  Max.   :0.0071            Max.   :0.0071             
##  NA's   :1131              NA's   :1123               
##  Day181cd4_IL17a_COV2.CON.S2 Day181cd4_IL17a_Wuhan.N Day181cd4_IL2_BA.4.5.S1
##  Min.   :0.0010              Min.   :0.0010          Min.   :0.0010         
##  1st Qu.:0.0010              1st Qu.:0.0010          1st Qu.:0.0172         
##  Median :0.0010              Median :0.0010          Median :0.0405         
##  Mean   :0.0013              Mean   :0.0013          Mean   :0.0680         
##  3rd Qu.:0.0010              3rd Qu.:0.0010          3rd Qu.:0.0705         
##  Max.   :0.0078              Max.   :0.0055          Max.   :0.5035         
##  NA's   :1123                NA's   :1137            NA's   :1128           
##  Day181cd4_IL2_BA.4.5.S2 Day181cd4_IL2_COV2.CON.S1 Day181cd4_IL2_COV2.CON.S2
##  Min.   :0.0010          Min.   :0.0010            Min.   :0.0010           
##  1st Qu.:0.0295          1st Qu.:0.0269            1st Qu.:0.0292           
##  Median :0.0521          Median :0.0508            Median :0.0596           
##  Mean   :0.0744          Mean   :0.0819            Mean   :0.0853           
##  3rd Qu.:0.0923          3rd Qu.:0.0891            3rd Qu.:0.1085           
##  Max.   :0.5274          Max.   :0.5672            Max.   :0.6013           
##  NA's   :1131            NA's   :1123              NA's   :1123             
##  Day181cd4_IL2_Wuhan.N Day181cd4_IL21_BA.4.5.S1 Day181cd4_IL21_BA.4.5.S2
##  Min.   :0.0010        Min.   :0.0010           Min.   :0.0010          
##  1st Qu.:0.0010        1st Qu.:0.0010           1st Qu.:0.0010          
##  Median :0.0052        Median :0.0037           Median :0.0027          
##  Mean   :0.0162        Mean   :0.0075           Mean   :0.0083          
##  3rd Qu.:0.0215        3rd Qu.:0.0094           3rd Qu.:0.0106          
##  Max.   :0.1080        Max.   :0.0791           Max.   :0.0803          
##  NA's   :1137          NA's   :1128             NA's   :1131            
##  Day181cd4_IL21_COV2.CON.S1 Day181cd4_IL21_COV2.CON.S2 Day181cd4_IL21_Wuhan.N
##  Min.   :0.0010             Min.   :0.0010             Min.   :0.0010        
##  1st Qu.:0.0010             1st Qu.:0.0010             1st Qu.:0.0010        
##  Median :0.0033             Median :0.0028             Median :0.0010        
##  Mean   :0.0085             Mean   :0.0087             Mean   :0.0038        
##  3rd Qu.:0.0097             3rd Qu.:0.0099             3rd Qu.:0.0047        
##  Max.   :0.0773             Max.   :0.0998             Max.   :0.0248        
##  NA's   :1123               NA's   :1123               NA's   :1137          
##  Day181cd4_IL4.154_BA.4.5.S1 Day181cd4_IL4.154_BA.4.5.S2
##  Min.   :0.0010              Min.   :0.0010             
##  1st Qu.:0.0010              1st Qu.:0.0010             
##  Median :0.0010              Median :0.0010             
##  Mean   :0.0017              Mean   :0.0015             
##  3rd Qu.:0.0010              3rd Qu.:0.0010             
##  Max.   :0.0255              Max.   :0.0148             
##  NA's   :1128                NA's   :1131               
##  Day181cd4_IL4.154_COV2.CON.S1 Day181cd4_IL4.154_COV2.CON.S2
##  Min.   :0.0010                Min.   :0.0010               
##  1st Qu.:0.0010                1st Qu.:0.0010               
##  Median :0.0010                Median :0.0010               
##  Mean   :0.0019                Mean   :0.0020               
##  3rd Qu.:0.0013                3rd Qu.:0.0012               
##  Max.   :0.0196                Max.   :0.0201               
##  NA's   :1123                  NA's   :1123                 
##  Day181cd4_IL4.154_Wuhan.N Day181cd4_IL4.IL5.IL13.154_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010                      
##  1st Qu.:0.0010            1st Qu.:0.0010                      
##  Median :0.0010            Median :0.0010                      
##  Mean   :0.0010            Mean   :0.0019                      
##  3rd Qu.:0.0010            3rd Qu.:0.0012                      
##  Max.   :0.0028            Max.   :0.0300                      
##  NA's   :1137              NA's   :1128                        
##  Day181cd4_IL4.IL5.IL13.154_BA.4.5.S2 Day181cd4_IL4.IL5.IL13.154_COV2.CON.S1
##  Min.   :0.0010                       Min.   :0.0010                        
##  1st Qu.:0.0010                       1st Qu.:0.0010                        
##  Median :0.0010                       Median :0.0010                        
##  Mean   :0.0017                       Mean   :0.0023                        
##  3rd Qu.:0.0011                       3rd Qu.:0.0015                        
##  Max.   :0.0202                       Max.   :0.0196                        
##  NA's   :1131                         NA's   :1123                          
##  Day181cd4_IL4.IL5.IL13.154_COV2.CON.S2 Day181cd4_IL4.IL5.IL13.154_Wuhan.N
##  Min.   :0.0010                         Min.   :0.0010                    
##  1st Qu.:0.0010                         1st Qu.:0.0010                    
##  Median :0.0010                         Median :0.0010                    
##  Mean   :0.0023                         Mean   :0.0011                    
##  3rd Qu.:0.0015                         3rd Qu.:0.0010                    
##  Max.   :0.0254                         Max.   :0.0041                    
##  NA's   :1123                           NA's   :1137                      
##  Day181cd4_IL5.IL13.154_BA.4.5.S1 Day181cd4_IL5.IL13.154_BA.4.5.S2
##  Min.   :0.0010                   Min.   :0.0010                  
##  1st Qu.:0.0010                   1st Qu.:0.0010                  
##  Median :0.0010                   Median :0.0010                  
##  Mean   :0.0014                   Mean   :0.0013                  
##  3rd Qu.:0.0010                   3rd Qu.:0.0010                  
##  Max.   :0.0135                   Max.   :0.0121                  
##  NA's   :1128                     NA's   :1131                    
##  Day181cd4_IL5.IL13.154_COV2.CON.S1 Day181cd4_IL5.IL13.154_COV2.CON.S2
##  Min.   :0.0010                     Min.   :0.0010                    
##  1st Qu.:0.0010                     1st Qu.:0.0010                    
##  Median :0.0010                     Median :0.0010                    
##  Mean   :0.0016                     Mean   :0.0017                    
##  3rd Qu.:0.0010                     3rd Qu.:0.0010                    
##  Max.   :0.0142                     Max.   :0.0173                    
##  NA's   :1123                       NA's   :1123                      
##  Day181cd4_IL5.IL13.154_Wuhan.N Day181cd4_TNFa_BA.4.5.S1
##  Min.   :0.0010                 Min.   :0.0010          
##  1st Qu.:0.0010                 1st Qu.:0.0161          
##  Median :0.0010                 Median :0.0416          
##  Mean   :0.0010                 Mean   :0.0844          
##  3rd Qu.:0.0010                 3rd Qu.:0.0993          
##  Max.   :0.0029                 Max.   :0.5945          
##  NA's   :1137                   NA's   :1128            
##  Day181cd4_TNFa_BA.4.5.S2 Day181cd4_TNFa_COV2.CON.S1 Day181cd4_TNFa_COV2.CON.S2
##  Min.   :0.0010           Min.   :0.0010             Min.   :0.0010            
##  1st Qu.:0.0247           1st Qu.:0.0178             1st Qu.:0.0282            
##  Median :0.0616           Median :0.0452             Median :0.0663            
##  Mean   :0.0906           Mean   :0.0921             Mean   :0.1051            
##  3rd Qu.:0.1078           3rd Qu.:0.1076             3rd Qu.:0.1264            
##  Max.   :0.6823           Max.   :0.7079             Max.   :0.7825            
##  NA's   :1131             NA's   :1123               NA's   :1123              
##  Day181cd4_TNFa_Wuhan.N Day181cd8_IFNg_BA.4.5.S1 Day181cd8_IFNg_BA.4.5.S2
##  Min.   :0.0010         Min.   :0.0010           Min.   :0.0010          
##  1st Qu.:0.0010         1st Qu.:0.0100           1st Qu.:0.0029          
##  Median :0.0010         Median :0.0515           Median :0.0118          
##  Mean   :0.0130         Mean   :0.4266           Mean   :0.0640          
##  3rd Qu.:0.0111         3rd Qu.:0.2807           3rd Qu.:0.0357          
##  Max.   :0.1425         Max.   :8.9409           Max.   :2.2259          
##  NA's   :1137           NA's   :1129             NA's   :1131            
##  Day181cd8_IFNg_COV2.CON.S1 Day181cd8_IFNg_COV2.CON.S2 Day181cd8_IFNg_Wuhan.N
##  Min.   :0.0010             Min.   :0.0010             Min.   :0.0010        
##  1st Qu.:0.0093             1st Qu.:0.0020             1st Qu.:0.0010        
##  Median :0.0741             Median :0.0135             Median :0.0049        
##  Mean   :0.3871             Mean   :0.0757             Mean   :0.0147        
##  3rd Qu.:0.2653             3rd Qu.:0.0410             3rd Qu.:0.0138        
##  Max.   :6.2853             Max.   :2.8235             Max.   :0.1989        
##  NA's   :1123               NA's   :1123               NA's   :1137          
##  Day181cd8_IFNg.IL2_BA.4.5.S1 Day181cd8_IFNg.IL2_BA.4.5.S2
##  Min.   :0.0010               Min.   :0.0010              
##  1st Qu.:0.0100               1st Qu.:0.0018              
##  Median :0.0515               Median :0.0122              
##  Mean   :0.4280               Mean   :0.0641              
##  3rd Qu.:0.2819               3rd Qu.:0.0354              
##  Max.   :8.9409               Max.   :2.2227              
##  NA's   :1129                 NA's   :1131                
##  Day181cd8_IFNg.IL2_COV2.CON.S1 Day181cd8_IFNg.IL2_COV2.CON.S2
##  Min.   :0.0010                 Min.   :0.0010                
##  1st Qu.:0.0077                 1st Qu.:0.0027                
##  Median :0.0762                 Median :0.0140                
##  Mean   :0.3886                 Mean   :0.0764                
##  3rd Qu.:0.2635                 3rd Qu.:0.0430                
##  Max.   :6.2827                 Max.   :2.8204                
##  NA's   :1123                   NA's   :1123                  
##  Day181cd8_IFNg.IL2_Wuhan.N Day181cd8_IFNg.IL2.TNFa_BA.4.5.S1
##  Min.   :0.0010             Min.   :0.0010                   
##  1st Qu.:0.0010             1st Qu.:0.0168                   
##  Median :0.0053             Median :0.0618                   
##  Mean   :0.0152             Mean   :0.4440                   
##  3rd Qu.:0.0148             3rd Qu.:0.2570                   
##  Max.   :0.1989             Max.   :9.1226                   
##  NA's   :1137               NA's   :1129                     
##  Day181cd8_IFNg.IL2.TNFa_BA.4.5.S2 Day181cd8_IFNg.IL2.TNFa_COV2.CON.S1
##  Min.   :0.0010                    Min.   :0.0010                     
##  1st Qu.:0.0011                    1st Qu.:0.0096                     
##  Median :0.0159                    Median :0.0880                     
##  Mean   :0.0695                    Mean   :0.4036                     
##  3rd Qu.:0.0423                    3rd Qu.:0.2629                     
##  Max.   :2.2399                    Max.   :6.3817                     
##  NA's   :1131                      NA's   :1123                       
##  Day181cd8_IFNg.IL2.TNFa_COV2.CON.S2 Day181cd8_IFNg.IL2.TNFa_Wuhan.N
##  Min.   :0.0010                      Min.   :0.0010                 
##  1st Qu.:0.0015                      1st Qu.:0.0010                 
##  Median :0.0157                      Median :0.0049                 
##  Mean   :0.0810                      Mean   :0.0159                 
##  3rd Qu.:0.0487                      3rd Qu.:0.0182                 
##  Max.   :2.8274                      Max.   :0.2013                 
##  NA's   :1123                        NA's   :1137                   
##  Day181cd8_IL2_BA.4.5.S1 Day181cd8_IL2_BA.4.5.S2 Day181cd8_IL2_COV2.CON.S1
##  Min.   :0.0010          Min.   :0.0010          Min.   :0.0010           
##  1st Qu.:0.0010          1st Qu.:0.0010          1st Qu.:0.0010           
##  Median :0.0065          Median :0.0010          Median :0.0079           
##  Mean   :0.0315          Mean   :0.0045          Mean   :0.0270           
##  3rd Qu.:0.0280          3rd Qu.:0.0064          3rd Qu.:0.0270           
##  Max.   :0.6543          Max.   :0.0331          Max.   :0.2259           
##  NA's   :1129            NA's   :1131            NA's   :1123             
##  Day181cd8_IL2_COV2.CON.S2 Day181cd8_IL2_Wuhan.N Day181cd8_TNFa_BA.4.5.S1
##  Min.   :0.0010            Min.   :0.0010        Min.   :0.0010          
##  1st Qu.:0.0010            1st Qu.:0.0010        1st Qu.:0.0137          
##  Median :0.0020            Median :0.0010        Median :0.0446          
##  Mean   :0.0061            Mean   :0.0050        Mean   :0.3630          
##  3rd Qu.:0.0075            3rd Qu.:0.0057        3rd Qu.:0.1751          
##  Max.   :0.0711            Max.   :0.0592        Max.   :8.0694          
##  NA's   :1123              NA's   :1137          NA's   :1129            
##  Day181cd8_TNFa_BA.4.5.S2 Day181cd8_TNFa_COV2.CON.S1 Day181cd8_TNFa_COV2.CON.S2
##  Min.   :0.0010           Min.   :0.0010             Min.   :0.0010            
##  1st Qu.:0.0010           1st Qu.:0.0049             1st Qu.:0.0010            
##  Median :0.0081           Median :0.0506             Median :0.0094            
##  Mean   :0.0518           Mean   :0.3073             Mean   :0.0602            
##  3rd Qu.:0.0332           3rd Qu.:0.1828             3rd Qu.:0.0320            
##  Max.   :1.6552           Max.   :5.3517             Max.   :2.1769            
##  NA's   :1131             NA's   :1123               NA's   :1123              
##  Day181cd8_TNFa_Wuhan.N Bcd4_154_BA.4.5.S1_resp Bcd4_154_BA.4.5.S2_resp
##  Min.   :0.0010         Min.   :0.0000          Min.   :0.0000         
##  1st Qu.:0.0010         1st Qu.:0.0000          1st Qu.:1.0000         
##  Median :0.0010         Median :1.0000          Median :1.0000         
##  Mean   :0.0080         Mean   :0.6614          Mean   :0.7989         
##  3rd Qu.:0.0104         3rd Qu.:1.0000          3rd Qu.:1.0000         
##  Max.   :0.1658         Max.   :1.0000          Max.   :1.0000         
##  NA's   :1137           NA's   :692             NA's   :710            
##  Bcd4_154_COV2.CON.S1_resp Bcd4_154_COV2.CON.S2_resp Bcd4_154_Wuhan.N_resp
##  Min.   :0.0000            Min.   :0.0000            Min.   :0.0000       
##  1st Qu.:1.0000            1st Qu.:1.0000            1st Qu.:0.0000       
##  Median :1.0000            Median :1.0000            Median :0.0000       
##  Mean   :0.8038            Mean   :0.8212            Mean   :0.1335       
##  3rd Qu.:1.0000            3rd Qu.:1.0000            3rd Qu.:0.0000       
##  Max.   :1.0000            Max.   :1.0000            Max.   :1.0000       
##  NA's   :686               NA's   :686               NA's   :745          
##  Bcd4_CXCR5.154_BA.4.5.S1_resp Bcd4_CXCR5.154_BA.4.5.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :0.0000               
##  Mean   :0.0071                Mean   :0.0091               
##  3rd Qu.:0.0000                3rd Qu.:0.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :700                   NA's   :713                  
##  Bcd4_CXCR5.154_COV2.CON.S1_resp Bcd4_CXCR5.154_COV2.CON.S2_resp
##  Min.   :0.0000                  Min.   :0.0000                 
##  1st Qu.:0.0000                  1st Qu.:0.0000                 
##  Median :0.0000                  Median :0.0000                 
##  Mean   :0.0243                  Mean   :0.0104                 
##  3rd Qu.:0.0000                  3rd Qu.:0.0000                 
##  Max.   :1.0000                  Max.   :1.0000                 
##  NA's   :687                     NA's   :686                    
##  Bcd4_CXCR5.154_Wuhan.N_resp Bcd4_CXCR5.IL21_BA.4.5.S1_resp
##  Min.   :0.0000              Min.   :0                     
##  1st Qu.:0.0000              1st Qu.:0                     
##  Median :0.0000              Median :0                     
##  Mean   :0.0039              Mean   :0                     
##  3rd Qu.:0.0000              3rd Qu.:0                     
##  Max.   :1.0000              Max.   :0                     
##  NA's   :750                 NA's   :700                   
##  Bcd4_CXCR5.IL21_BA.4.5.S2_resp Bcd4_CXCR5.IL21_COV2.CON.S1_resp
##  Min.   :0                      Min.   :0                       
##  1st Qu.:0                      1st Qu.:0                       
##  Median :0                      Median :0                       
##  Mean   :0                      Mean   :0                       
##  3rd Qu.:0                      3rd Qu.:0                       
##  Max.   :0                      Max.   :0                       
##  NA's   :713                    NA's   :687                     
##  Bcd4_CXCR5.IL21_COV2.CON.S2_resp Bcd4_CXCR5.IL21_Wuhan.N_resp
##  Min.   :0                        Min.   :0.000               
##  1st Qu.:0                        1st Qu.:0.000               
##  Median :0                        Median :0.000               
##  Mean   :0                        Mean   :0.002               
##  3rd Qu.:0                        3rd Qu.:0.000               
##  Max.   :0                        Max.   :1.000               
##  NA's   :686                      NA's   :750                 
##  Bcd4_IFNg_BA.4.5.S1_resp Bcd4_IFNg_BA.4.5.S2_resp Bcd4_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000           Min.   :0.0000           Min.   :0.0000            
##  1st Qu.:0.0000           1st Qu.:0.0000           1st Qu.:0.0000            
##  Median :1.0000           Median :1.0000           Median :1.0000            
##  Mean   :0.5105           Mean   :0.6775           Mean   :0.6545            
##  3rd Qu.:1.0000           3rd Qu.:1.0000           3rd Qu.:1.0000            
##  Max.   :1.0000           Max.   :1.0000           Max.   :1.0000            
##  NA's   :692              NA's   :710              NA's   :686               
##  Bcd4_IFNg_COV2.CON.S2_resp Bcd4_IFNg_Wuhan.N_resp Bcd4_IFNg.IL2_BA.4.5.S1_resp
##  Min.   :0.0000             Min.   :0.0000         Min.   :0.0000              
##  1st Qu.:0.0000             1st Qu.:0.0000         1st Qu.:0.0000              
##  Median :1.0000             Median :0.0000         Median :1.0000              
##  Mean   :0.7326             Mean   :0.0832         Mean   :0.5912              
##  3rd Qu.:1.0000             3rd Qu.:0.0000         3rd Qu.:1.0000              
##  Max.   :1.0000             Max.   :1.0000         Max.   :1.0000              
##  NA's   :686                NA's   :745            NA's   :692                 
##  Bcd4_IFNg.IL2_BA.4.5.S2_resp Bcd4_IFNg.IL2_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :1.0000               Median :1.0000                
##  Mean   :0.7246               Mean   :0.7101                
##  3rd Qu.:1.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :710                  NA's   :686                   
##  Bcd4_IFNg.IL2_COV2.CON.S2_resp Bcd4_IFNg.IL2_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:1.0000                 1st Qu.:0.0000            
##  Median :1.0000                 Median :0.0000            
##  Mean   :0.7691                 Mean   :0.1103            
##  3rd Qu.:1.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :686                    NA's   :745               
##  Bcd4_IFNg.IL2.154_BA.4.5.S1_resp Bcd4_IFNg.IL2.154_BA.4.5.S2_resp
##  Min.   :0.0000                   Min.   :0.0000                  
##  1st Qu.:0.0000                   1st Qu.:0.0000                  
##  Median :1.0000                   Median :1.0000                  
##  Mean   :0.6211                   Mean   :0.7428                  
##  3rd Qu.:1.0000                   3rd Qu.:1.0000                  
##  Max.   :1.0000                   Max.   :1.0000                  
##  NA's   :692                      NA's   :710                     
##  Bcd4_IFNg.IL2.154_COV2.CON.S1_resp Bcd4_IFNg.IL2.154_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:0.0000                     1st Qu.:1.0000                    
##  Median :1.0000                     Median :1.0000                    
##  Mean   :0.7274                     Mean   :0.7691                    
##  3rd Qu.:1.0000                     3rd Qu.:1.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :686                        NA's   :686                       
##  Bcd4_IFNg.IL2.154_Wuhan.N_resp Bcd4_IL17a_BA.4.5.S1_resp
##  Min.   :0.000                  Min.   :0                
##  1st Qu.:0.000                  1st Qu.:0                
##  Median :0.000                  Median :0                
##  Mean   :0.118                  Mean   :0                
##  3rd Qu.:0.000                  3rd Qu.:0                
##  Max.   :1.000                  Max.   :0                
##  NA's   :745                    NA's   :692              
##  Bcd4_IL17a_BA.4.5.S2_resp Bcd4_IL17a_COV2.CON.S1_resp
##  Min.   :0                 Min.   :0                  
##  1st Qu.:0                 1st Qu.:0                  
##  Median :0                 Median :0                  
##  Mean   :0                 Mean   :0                  
##  3rd Qu.:0                 3rd Qu.:0                  
##  Max.   :0                 Max.   :0                  
##  NA's   :710               NA's   :686                
##  Bcd4_IL17a_COV2.CON.S2_resp Bcd4_IL17a_Wuhan.N_resp Bcd4_IL2_BA.4.5.S1_resp
##  Min.   :0                   Min.   :0               Min.   :0.0000         
##  1st Qu.:0                   1st Qu.:0               1st Qu.:0.0000         
##  Median :0                   Median :0               Median :1.0000         
##  Mean   :0                   Mean   :0               Mean   :0.5351         
##  3rd Qu.:0                   3rd Qu.:0               3rd Qu.:1.0000         
##  Max.   :0                   Max.   :0               Max.   :1.0000         
##  NA's   :686                 NA's   :745             NA's   :692            
##  Bcd4_IL2_BA.4.5.S2_resp Bcd4_IL2_COV2.CON.S1_resp Bcd4_IL2_COV2.CON.S2_resp
##  Min.   :0.0000          Min.   :0.0000            Min.   :0.0000           
##  1st Qu.:0.0000          1st Qu.:0.0000            1st Qu.:0.0000           
##  Median :1.0000          Median :1.0000            Median :1.0000           
##  Mean   :0.6467          Mean   :0.6458            Mean   :0.6997           
##  3rd Qu.:1.0000          3rd Qu.:1.0000            3rd Qu.:1.0000           
##  Max.   :1.0000          Max.   :1.0000            Max.   :1.0000           
##  NA's   :710             NA's   :686               NA's   :686              
##  Bcd4_IL2_Wuhan.N_resp Bcd4_IL21_BA.4.5.S1_resp Bcd4_IL21_BA.4.5.S2_resp
##  Min.   :0.0000        Min.   :0.0000           Min.   :0.0000          
##  1st Qu.:0.0000        1st Qu.:0.0000           1st Qu.:0.0000          
##  Median :0.0000        Median :0.0000           Median :0.0000          
##  Mean   :0.0851        Mean   :0.0053           Mean   :0.0054          
##  3rd Qu.:0.0000        3rd Qu.:0.0000           3rd Qu.:0.0000          
##  Max.   :1.0000        Max.   :1.0000           Max.   :1.0000          
##  NA's   :745           NA's   :692              NA's   :710             
##  Bcd4_IL21_COV2.CON.S1_resp Bcd4_IL21_COV2.CON.S2_resp Bcd4_IL21_Wuhan.N_resp
##  Min.   :0.0000             Min.   :0.0000             Min.   :0.0000        
##  1st Qu.:0.0000             1st Qu.:0.0000             1st Qu.:0.0000        
##  Median :0.0000             Median :0.0000             Median :0.0000        
##  Mean   :0.0104             Mean   :0.0104             Mean   :0.0039        
##  3rd Qu.:0.0000             3rd Qu.:0.0000             3rd Qu.:0.0000        
##  Max.   :1.0000             Max.   :1.0000             Max.   :1.0000        
##  NA's   :686                NA's   :686                NA's   :745           
##  Bcd4_IL4.154_BA.4.5.S1_resp Bcd4_IL4.154_BA.4.5.S2_resp
##  Min.   :0                   Min.   :0.0000             
##  1st Qu.:0                   1st Qu.:0.0000             
##  Median :0                   Median :0.0000             
##  Mean   :0                   Mean   :0.0018             
##  3rd Qu.:0                   3rd Qu.:0.0000             
##  Max.   :0                   Max.   :1.0000             
##  NA's   :692                 NA's   :710                
##  Bcd4_IL4.154_COV2.CON.S1_resp Bcd4_IL4.154_COV2.CON.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :0.0000               
##  Mean   :0.0052                Mean   :0.0035               
##  3rd Qu.:0.0000                3rd Qu.:0.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :686                   NA's   :686                  
##  Bcd4_IL4.154_Wuhan.N_resp Bcd4_IL4.IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0                 Min.   :0.0000                      
##  1st Qu.:0                 1st Qu.:0.0000                      
##  Median :0                 Median :0.0000                      
##  Mean   :0                 Mean   :0.0035                      
##  3rd Qu.:0                 3rd Qu.:0.0000                      
##  Max.   :0                 Max.   :1.0000                      
##  NA's   :745               NA's   :692                         
##  Bcd4_IL4.IL5.IL13.154_BA.4.5.S2_resp Bcd4_IL4.IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0.0000                       Min.   :0.0000                        
##  1st Qu.:0.0000                       1st Qu.:0.0000                        
##  Median :0.0000                       Median :0.0000                        
##  Mean   :0.0072                       Mean   :0.0069                        
##  3rd Qu.:0.0000                       3rd Qu.:0.0000                        
##  Max.   :1.0000                       Max.   :1.0000                        
##  NA's   :710                          NA's   :686                           
##  Bcd4_IL4.IL5.IL13.154_COV2.CON.S2_resp Bcd4_IL4.IL5.IL13.154_Wuhan.N_resp
##  Min.   :0.0000                         Min.   :0                         
##  1st Qu.:0.0000                         1st Qu.:0                         
##  Median :0.0000                         Median :0                         
##  Mean   :0.0069                         Mean   :0                         
##  3rd Qu.:0.0000                         3rd Qu.:0                         
##  Max.   :1.0000                         Max.   :0                         
##  NA's   :686                            NA's   :745                       
##  Bcd4_IL5.IL13.154_BA.4.5.S1_resp Bcd4_IL5.IL13.154_BA.4.5.S2_resp
##  Min.   :0.0000                   Min.   :0                       
##  1st Qu.:0.0000                   1st Qu.:0                       
##  Median :0.0000                   Median :0                       
##  Mean   :0.0035                   Mean   :0                       
##  3rd Qu.:0.0000                   3rd Qu.:0                       
##  Max.   :1.0000                   Max.   :0                       
##  NA's   :692                      NA's   :710                     
##  Bcd4_IL5.IL13.154_COV2.CON.S1_resp Bcd4_IL5.IL13.154_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:0.0000                     1st Qu.:0.0000                    
##  Median :0.0000                     Median :0.0000                    
##  Mean   :0.0017                     Mean   :0.0017                    
##  3rd Qu.:0.0000                     3rd Qu.:0.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :686                        NA's   :686                       
##  Bcd4_IL5.IL13.154_Wuhan.N_resp Bcd4_TNFa_BA.4.5.S1_resp
##  Min.   :0                      Min.   :0.0000          
##  1st Qu.:0                      1st Qu.:0.0000          
##  Median :0                      Median :0.0000          
##  Mean   :0                      Mean   :0.3491          
##  3rd Qu.:0                      3rd Qu.:1.0000          
##  Max.   :0                      Max.   :1.0000          
##  NA's   :745                    NA's   :692             
##  Bcd4_TNFa_BA.4.5.S2_resp Bcd4_TNFa_COV2.CON.S1_resp Bcd4_TNFa_COV2.CON.S2_resp
##  Min.   :0.0000           Min.   :0.0000             Min.   :0.0000            
##  1st Qu.:0.0000           1st Qu.:0.0000             1st Qu.:0.0000            
##  Median :0.0000           Median :0.0000             Median :0.0000            
##  Mean   :0.4312           Mean   :0.4219             Mean   :0.4774            
##  3rd Qu.:1.0000           3rd Qu.:1.0000             3rd Qu.:1.0000            
##  Max.   :1.0000           Max.   :1.0000             Max.   :1.0000            
##  NA's   :710              NA's   :686                NA's   :686               
##  Bcd4_TNFa_Wuhan.N_resp Bcd8_IFNg_BA.4.5.S1_resp Bcd8_IFNg_BA.4.5.S2_resp
##  Min.   :0.0000         Min.   :0.0000           Min.   :0.0000          
##  1st Qu.:0.0000         1st Qu.:0.0000           1st Qu.:0.0000          
##  Median :0.0000         Median :0.0000           Median :0.0000          
##  Mean   :0.0387         Mean   :0.3662           Mean   :0.1866          
##  3rd Qu.:0.0000         3rd Qu.:1.0000           3rd Qu.:0.0000          
##  Max.   :1.0000         Max.   :1.0000           Max.   :1.0000          
##  NA's   :745            NA's   :694              NA's   :710             
##  Bcd8_IFNg_COV2.CON.S1_resp Bcd8_IFNg_COV2.CON.S2_resp Bcd8_IFNg_Wuhan.N_resp
##  Min.   :0.0000             Min.   :0.0000             Min.   :0.0000        
##  1st Qu.:0.0000             1st Qu.:0.0000             1st Qu.:0.0000        
##  Median :0.0000             Median :0.0000             Median :0.0000        
##  Mean   :0.3785             Mean   :0.1528             Mean   :0.0349        
##  3rd Qu.:1.0000             3rd Qu.:0.0000             3rd Qu.:0.0000        
##  Max.   :1.0000             Max.   :1.0000             Max.   :1.0000        
##  NA's   :686                NA's   :686                NA's   :746           
##  Bcd8_IFNg.IL2_BA.4.5.S1_resp Bcd8_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :0.0000               Median :0.0000              
##  Mean   :0.3592               Mean   :0.1793              
##  3rd Qu.:1.0000               3rd Qu.:0.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :694                  NA's   :710                 
##  Bcd8_IFNg.IL2_COV2.CON.S1_resp Bcd8_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :0.0000                 Median :0.0000                
##  Mean   :0.3767                 Mean   :0.1424                
##  3rd Qu.:1.0000                 3rd Qu.:0.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :686                    NA's   :686                   
##  Bcd8_IFNg.IL2_Wuhan.N_resp Bcd8_IFNg.IL2.TNFa_BA.4.5.S1_resp
##  Min.   :0.0000             Min.   :0.000                    
##  1st Qu.:0.0000             1st Qu.:0.000                    
##  Median :0.0000             Median :0.000                    
##  Mean   :0.0349             Mean   :0.338                    
##  3rd Qu.:0.0000             3rd Qu.:1.000                    
##  Max.   :1.0000             Max.   :1.000                    
##  NA's   :746                NA's   :694                      
##  Bcd8_IFNg.IL2.TNFa_BA.4.5.S2_resp Bcd8_IFNg.IL2.TNFa_COV2.CON.S1_resp
##  Min.   :0.0000                    Min.   :0.0000                     
##  1st Qu.:0.0000                    1st Qu.:0.0000                     
##  Median :0.0000                    Median :0.0000                     
##  Mean   :0.1721                    Mean   :0.3576                     
##  3rd Qu.:0.0000                    3rd Qu.:1.0000                     
##  Max.   :1.0000                    Max.   :1.0000                     
##  NA's   :710                       NA's   :686                        
##  Bcd8_IFNg.IL2.TNFa_COV2.CON.S2_resp Bcd8_IFNg.IL2.TNFa_Wuhan.N_resp
##  Min.   :0.0000                      Min.   :0.0000                 
##  1st Qu.:0.0000                      1st Qu.:0.0000                 
##  Median :0.0000                      Median :0.0000                 
##  Mean   :0.1319                      Mean   :0.0252                 
##  3rd Qu.:0.0000                      3rd Qu.:0.0000                 
##  Max.   :1.0000                      Max.   :1.0000                 
##  NA's   :686                         NA's   :746                    
##  Bcd8_IL2_BA.4.5.S1_resp Bcd8_IL2_BA.4.5.S2_resp Bcd8_IL2_COV2.CON.S1_resp
##  Min.   :0.0000          Min.   :0.0000          Min.   :0.0000           
##  1st Qu.:0.0000          1st Qu.:0.0000          1st Qu.:0.0000           
##  Median :0.0000          Median :0.0000          Median :0.0000           
##  Mean   :0.1144          Mean   :0.0236          Mean   :0.1059           
##  3rd Qu.:0.0000          3rd Qu.:0.0000          3rd Qu.:0.0000           
##  Max.   :1.0000          Max.   :1.0000          Max.   :1.0000           
##  NA's   :694             NA's   :710             NA's   :686              
##  Bcd8_IL2_COV2.CON.S2_resp Bcd8_IL2_Wuhan.N_resp Bcd8_TNFa_BA.4.5.S1_resp
##  Min.   :0.0000            Min.   :0.0000        Min.   :0.0000          
##  1st Qu.:0.0000            1st Qu.:0.0000        1st Qu.:0.0000          
##  Median :0.0000            Median :0.0000        Median :0.0000          
##  Mean   :0.0278            Mean   :0.0155        Mean   :0.2975          
##  3rd Qu.:0.0000            3rd Qu.:0.0000        3rd Qu.:1.0000          
##  Max.   :1.0000            Max.   :1.0000        Max.   :1.0000          
##  NA's   :686               NA's   :746           NA's   :694             
##  Bcd8_TNFa_BA.4.5.S2_resp Bcd8_TNFa_COV2.CON.S1_resp Bcd8_TNFa_COV2.CON.S2_resp
##  Min.   :0.0000           Min.   :0.0000             Min.   :0.0000            
##  1st Qu.:0.0000           1st Qu.:0.0000             1st Qu.:0.0000            
##  Median :0.0000           Median :0.0000             Median :0.0000            
##  Mean   :0.1322           Mean   :0.2847             Mean   :0.1059            
##  3rd Qu.:0.0000           3rd Qu.:1.0000             3rd Qu.:0.0000            
##  Max.   :1.0000           Max.   :1.0000             Max.   :1.0000            
##  NA's   :710              NA's   :686                NA's   :686               
##  Bcd8_TNFa_Wuhan.N_resp Day15cd4_154_BA.4.5.S1_resp Day15cd4_154_BA.4.5.S2_resp
##  Min.   :0.0000         Min.   :0.000               Min.   :0.0000             
##  1st Qu.:0.0000         1st Qu.:1.000               1st Qu.:1.0000             
##  Median :0.0000         Median :1.000               Median :1.0000             
##  Mean   :0.0116         Mean   :0.884               Mean   :0.9159             
##  3rd Qu.:0.0000         3rd Qu.:1.000               3rd Qu.:1.0000             
##  Max.   :1.0000         Max.   :1.000               Max.   :1.0000             
##  NA's   :746            NA's   :693                 NA's   :703                
##  Day15cd4_154_COV2.CON.S1_resp Day15cd4_154_COV2.CON.S2_resp
##  Min.   :0.000                 Min.   :0.0000               
##  1st Qu.:1.000                 1st Qu.:1.0000               
##  Median :1.000                 Median :1.0000               
##  Mean   :0.934                 Mean   :0.9167               
##  3rd Qu.:1.000                 3rd Qu.:1.0000               
##  Max.   :1.000                 Max.   :1.0000               
##  NA's   :686                   NA's   :686                  
##  Day15cd4_154_Wuhan.N_resp Day15cd4_CXCR5.154_BA.4.5.S1_resp
##  Min.   :0.0000            Min.   :0.0000                   
##  1st Qu.:0.0000            1st Qu.:0.0000                   
##  Median :0.0000            Median :0.0000                   
##  Mean   :0.1394            Mean   :0.0677                   
##  3rd Qu.:0.0000            3rd Qu.:0.0000                   
##  Max.   :1.0000            Max.   :1.0000                   
##  NA's   :717               NA's   :701                      
##  Day15cd4_CXCR5.154_BA.4.5.S2_resp Day15cd4_CXCR5.154_COV2.CON.S1_resp
##  Min.   :0.0000                    Min.   :0.0000                     
##  1st Qu.:0.0000                    1st Qu.:0.0000                     
##  Median :0.0000                    Median :0.0000                     
##  Mean   :0.0522                    Mean   :0.1304                     
##  3rd Qu.:0.0000                    3rd Qu.:0.0000                     
##  Max.   :1.0000                    Max.   :1.0000                     
##  NA's   :706                       NA's   :687                        
##  Day15cd4_CXCR5.154_COV2.CON.S2_resp Day15cd4_CXCR5.154_Wuhan.N_resp
##  Min.   :0.0000                      Min.   :0.0000                 
##  1st Qu.:0.0000                      1st Qu.:0.0000                 
##  Median :0.0000                      Median :0.0000                 
##  Mean   :0.0799                      Mean   :0.0019                 
##  3rd Qu.:0.0000                      3rd Qu.:0.0000                 
##  Max.   :1.0000                      Max.   :1.0000                 
##  NA's   :686                         NA's   :723                    
##  Day15cd4_CXCR5.IL21_BA.4.5.S1_resp Day15cd4_CXCR5.IL21_BA.4.5.S2_resp
##  Min.   :0                          Min.   :0                         
##  1st Qu.:0                          1st Qu.:0                         
##  Median :0                          Median :0                         
##  Mean   :0                          Mean   :0                         
##  3rd Qu.:0                          3rd Qu.:0                         
##  Max.   :0                          Max.   :0                         
##  NA's   :701                        NA's   :706                       
##  Day15cd4_CXCR5.IL21_COV2.CON.S1_resp Day15cd4_CXCR5.IL21_COV2.CON.S2_resp
##  Min.   :0.0000                       Min.   :0                           
##  1st Qu.:0.0000                       1st Qu.:0                           
##  Median :0.0000                       Median :0                           
##  Mean   :0.0035                       Mean   :0                           
##  3rd Qu.:0.0000                       3rd Qu.:0                           
##  Max.   :1.0000                       Max.   :0                           
##  NA's   :687                          NA's   :686                         
##  Day15cd4_CXCR5.IL21_Wuhan.N_resp Day15cd4_IFNg_BA.4.5.S1_resp
##  Min.   :0                        Min.   :0.0000              
##  1st Qu.:0                        1st Qu.:1.0000              
##  Median :0                        Median :1.0000              
##  Mean   :0                        Mean   :0.8032              
##  3rd Qu.:0                        3rd Qu.:1.0000              
##  Max.   :0                        Max.   :1.0000              
##  NA's   :723                      NA's   :693                 
##  Day15cd4_IFNg_BA.4.5.S2_resp Day15cd4_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:1.0000               1st Qu.:1.0000                
##  Median :1.0000               Median :1.0000                
##  Mean   :0.8962               Mean   :0.8715                
##  3rd Qu.:1.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :703                  NA's   :686                   
##  Day15cd4_IFNg_COV2.CON.S2_resp Day15cd4_IFNg_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:1.0000                 1st Qu.:0.0000            
##  Median :1.0000                 Median :0.0000            
##  Mean   :0.8958                 Mean   :0.0936            
##  3rd Qu.:1.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :686                    NA's   :717               
##  Day15cd4_IFNg.IL2_BA.4.5.S1_resp Day15cd4_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000                   Min.   :0.0000                  
##  1st Qu.:1.0000                   1st Qu.:1.0000                  
##  Median :1.0000                   Median :1.0000                  
##  Mean   :0.8172                   Mean   :0.8998                  
##  3rd Qu.:1.0000                   3rd Qu.:1.0000                  
##  Max.   :1.0000                   Max.   :1.0000                  
##  NA's   :693                      NA's   :703                     
##  Day15cd4_IFNg.IL2_COV2.CON.S1_resp Day15cd4_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:1.0000                     1st Qu.:1.0000                    
##  Median :1.0000                     Median :1.0000                    
##  Mean   :0.8993                     Mean   :0.9028                    
##  3rd Qu.:1.0000                     3rd Qu.:1.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :686                        NA's   :686                       
##  Day15cd4_IFNg.IL2_Wuhan.N_resp Day15cd4_IFNg.IL2.154_BA.4.5.S1_resp
##  Min.   :0.0000                 Min.   :0.0000                      
##  1st Qu.:0.0000                 1st Qu.:1.0000                      
##  Median :0.0000                 Median :1.0000                      
##  Mean   :0.1064                 Mean   :0.8383                      
##  3rd Qu.:0.0000                 3rd Qu.:1.0000                      
##  Max.   :1.0000                 Max.   :1.0000                      
##  NA's   :717                    NA's   :693                         
##  Day15cd4_IFNg.IL2.154_BA.4.5.S2_resp Day15cd4_IFNg.IL2.154_COV2.CON.S1_resp
##  Min.   :0.000                        Min.   :0.0000                        
##  1st Qu.:1.000                        1st Qu.:1.0000                        
##  Median :1.000                        Median :1.0000                        
##  Mean   :0.898                        Mean   :0.9097                        
##  3rd Qu.:1.000                        3rd Qu.:1.0000                        
##  Max.   :1.000                        Max.   :1.0000                        
##  NA's   :703                          NA's   :686                           
##  Day15cd4_IFNg.IL2.154_COV2.CON.S2_resp Day15cd4_IFNg.IL2.154_Wuhan.N_resp
##  Min.   :0.0000                         Min.   :0.0000                    
##  1st Qu.:1.0000                         1st Qu.:0.0000                    
##  Median :1.0000                         Median :0.0000                    
##  Mean   :0.9045                         Mean   :0.1156                    
##  3rd Qu.:1.0000                         3rd Qu.:0.0000                    
##  Max.   :1.0000                         Max.   :1.0000                    
##  NA's   :686                            NA's   :717                       
##  Day15cd4_IL17a_BA.4.5.S1_resp Day15cd4_IL17a_BA.4.5.S2_resp
##  Min.   :0                     Min.   :0                    
##  1st Qu.:0                     1st Qu.:0                    
##  Median :0                     Median :0                    
##  Mean   :0                     Mean   :0                    
##  3rd Qu.:0                     3rd Qu.:0                    
##  Max.   :0                     Max.   :0                    
##  NA's   :693                   NA's   :703                  
##  Day15cd4_IL17a_COV2.CON.S1_resp Day15cd4_IL17a_COV2.CON.S2_resp
##  Min.   :0                       Min.   :0                      
##  1st Qu.:0                       1st Qu.:0                      
##  Median :0                       Median :0                      
##  Mean   :0                       Mean   :0                      
##  3rd Qu.:0                       3rd Qu.:0                      
##  Max.   :0                       Max.   :0                      
##  NA's   :686                     NA's   :686                    
##  Day15cd4_IL17a_Wuhan.N_resp Day15cd4_IL2_BA.4.5.S1_resp
##  Min.   :0                   Min.   :0.0000             
##  1st Qu.:0                   1st Qu.:0.0000             
##  Median :0                   Median :1.0000             
##  Mean   :0                   Mean   :0.6819             
##  3rd Qu.:0                   3rd Qu.:1.0000             
##  Max.   :0                   Max.   :1.0000             
##  NA's   :717                 NA's   :693                
##  Day15cd4_IL2_BA.4.5.S2_resp Day15cd4_IL2_COV2.CON.S1_resp
##  Min.   :0.00                Min.   :0.0000               
##  1st Qu.:1.00                1st Qu.:1.0000               
##  Median :1.00                Median :1.0000               
##  Mean   :0.78                Mean   :0.7778               
##  3rd Qu.:1.00                3rd Qu.:1.0000               
##  Max.   :1.00                Max.   :1.0000               
##  NA's   :703                 NA's   :686                  
##  Day15cd4_IL2_COV2.CON.S2_resp Day15cd4_IL2_Wuhan.N_resp
##  Min.   :0.0000                Min.   :0.0000           
##  1st Qu.:1.0000                1st Qu.:0.0000           
##  Median :1.0000                Median :0.0000           
##  Mean   :0.7969                Mean   :0.0844           
##  3rd Qu.:1.0000                3rd Qu.:0.0000           
##  Max.   :1.0000                Max.   :1.0000           
##  NA's   :686                   NA's   :717              
##  Day15cd4_IL21_BA.4.5.S1_resp Day15cd4_IL21_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :0.0000               Median :0.0000              
##  Mean   :0.1195               Mean   :0.1914              
##  3rd Qu.:0.0000               3rd Qu.:0.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :693                  NA's   :703                 
##  Day15cd4_IL21_COV2.CON.S1_resp Day15cd4_IL21_COV2.CON.S2_resp
##  Min.   :0.000                  Min.   :0.0000                
##  1st Qu.:0.000                  1st Qu.:0.0000                
##  Median :0.000                  Median :0.0000                
##  Mean   :0.184                  Mean   :0.2257                
##  3rd Qu.:0.000                  3rd Qu.:0.0000                
##  Max.   :1.000                  Max.   :1.0000                
##  NA's   :686                    NA's   :686                   
##  Day15cd4_IL21_Wuhan.N_resp Day15cd4_IL4.154_BA.4.5.S1_resp
##  Min.   :0.0000             Min.   :0.0000                 
##  1st Qu.:0.0000             1st Qu.:0.0000                 
##  Median :0.0000             Median :0.0000                 
##  Mean   :0.0055             Mean   :0.0088                 
##  3rd Qu.:0.0000             3rd Qu.:0.0000                 
##  Max.   :1.0000             Max.   :1.0000                 
##  NA's   :717                NA's   :693                    
##  Day15cd4_IL4.154_BA.4.5.S2_resp Day15cd4_IL4.154_COV2.CON.S1_resp
##  Min.   :0.0000                  Min.   :0.0000                   
##  1st Qu.:0.0000                  1st Qu.:0.0000                   
##  Median :0.0000                  Median :0.0000                   
##  Mean   :0.0054                  Mean   :0.0243                   
##  3rd Qu.:0.0000                  3rd Qu.:0.0000                   
##  Max.   :1.0000                  Max.   :1.0000                   
##  NA's   :703                     NA's   :686                      
##  Day15cd4_IL4.154_COV2.CON.S2_resp Day15cd4_IL4.154_Wuhan.N_resp
##  Min.   :0.0000                    Min.   :0                    
##  1st Qu.:0.0000                    1st Qu.:0                    
##  Median :0.0000                    Median :0                    
##  Mean   :0.0087                    Mean   :0                    
##  3rd Qu.:0.0000                    3rd Qu.:0                    
##  Max.   :1.0000                    Max.   :0                    
##  NA's   :686                       NA's   :717                  
##  Day15cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0.0000                          
##  1st Qu.:0.0000                          
##  Median :0.0000                          
##  Mean   :0.0193                          
##  3rd Qu.:0.0000                          
##  Max.   :1.0000                          
##  NA's   :693                             
##  Day15cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp
##  Min.   :0.0000                          
##  1st Qu.:0.0000                          
##  Median :0.0000                          
##  Mean   :0.0179                          
##  3rd Qu.:0.0000                          
##  Max.   :1.0000                          
##  NA's   :703                             
##  Day15cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0.0000                            
##  1st Qu.:0.0000                            
##  Median :0.0000                            
##  Mean   :0.0365                            
##  3rd Qu.:0.0000                            
##  Max.   :1.0000                            
##  NA's   :686                               
##  Day15cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp
##  Min.   :0.0000                            
##  1st Qu.:0.0000                            
##  Median :0.0000                            
##  Mean   :0.0226                            
##  3rd Qu.:0.0000                            
##  Max.   :1.0000                            
##  NA's   :686                               
##  Day15cd4_IL4.IL5.IL13.154_Wuhan.N_resp Day15cd4_IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0                              Min.   :0.0000                      
##  1st Qu.:0                              1st Qu.:0.0000                      
##  Median :0                              Median :0.0000                      
##  Mean   :0                              Mean   :0.0053                      
##  3rd Qu.:0                              3rd Qu.:0.0000                      
##  Max.   :0                              Max.   :1.0000                      
##  NA's   :717                            NA's   :693                         
##  Day15cd4_IL5.IL13.154_BA.4.5.S2_resp Day15cd4_IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0.0000                       Min.   :0.0000                        
##  1st Qu.:0.0000                       1st Qu.:0.0000                        
##  Median :0.0000                       Median :0.0000                        
##  Mean   :0.0054                       Mean   :0.0122                        
##  3rd Qu.:0.0000                       3rd Qu.:0.0000                        
##  Max.   :1.0000                       Max.   :1.0000                        
##  NA's   :703                          NA's   :686                           
##  Day15cd4_IL5.IL13.154_COV2.CON.S2_resp Day15cd4_IL5.IL13.154_Wuhan.N_resp
##  Min.   :0.0000                         Min.   :0                         
##  1st Qu.:0.0000                         1st Qu.:0                         
##  Median :0.0000                         Median :0                         
##  Mean   :0.0035                         Mean   :0                         
##  3rd Qu.:0.0000                         3rd Qu.:0                         
##  Max.   :1.0000                         Max.   :0                         
##  NA's   :686                            NA's   :717                       
##  Day15cd4_TNFa_BA.4.5.S1_resp Day15cd4_TNFa_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :1.0000               Median :1.0000              
##  Mean   :0.5431               Mean   :0.6279              
##  3rd Qu.:1.0000               3rd Qu.:1.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :693                  NA's   :703                 
##  Day15cd4_TNFa_COV2.CON.S1_resp Day15cd4_TNFa_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :1.0000                 Median :1.0000                
##  Mean   :0.5972                 Mean   :0.6545                
##  3rd Qu.:1.0000                 3rd Qu.:1.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :686                    NA's   :686                   
##  Day15cd4_TNFa_Wuhan.N_resp Day15cd8_IFNg_BA.4.5.S1_resp
##  Min.   :0.0000             Min.   :0.0000              
##  1st Qu.:0.0000             1st Qu.:0.0000              
##  Median :0.0000             Median :0.0000              
##  Mean   :0.0275             Mean   :0.4586              
##  3rd Qu.:0.0000             3rd Qu.:1.0000              
##  Max.   :1.0000             Max.   :1.0000              
##  NA's   :717                NA's   :695                 
##  Day15cd8_IFNg_BA.4.5.S2_resp Day15cd8_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :0.0000               Median :0.0000                
##  Mean   :0.2576               Mean   :0.4991                
##  3rd Qu.:1.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :703                  NA's   :687                   
##  Day15cd8_IFNg_COV2.CON.S2_resp Day15cd8_IFNg_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:0.0000                 1st Qu.:0.0000            
##  Median :0.0000                 Median :0.0000            
##  Mean   :0.2326                 Mean   :0.0331            
##  3rd Qu.:0.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :686                    NA's   :719               
##  Day15cd8_IFNg.IL2_BA.4.5.S1_resp Day15cd8_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.000                    Min.   :0.0000                  
##  1st Qu.:0.000                    1st Qu.:0.0000                  
##  Median :0.000                    Median :0.0000                  
##  Mean   :0.448                    Mean   :0.2504                  
##  3rd Qu.:1.000                    3rd Qu.:0.5000                  
##  Max.   :1.000                    Max.   :1.0000                  
##  NA's   :695                      NA's   :703                     
##  Day15cd8_IFNg.IL2_COV2.CON.S1_resp Day15cd8_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:0.0000                     1st Qu.:0.0000                    
##  Median :0.0000                     Median :0.0000                    
##  Mean   :0.4922                     Mean   :0.2257                    
##  3rd Qu.:1.0000                     3rd Qu.:0.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :687                        NA's   :686                       
##  Day15cd8_IFNg.IL2_Wuhan.N_resp Day15cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp
##  Min.   :0.000                  Min.   :0.0000                       
##  1st Qu.:0.000                  1st Qu.:0.0000                       
##  Median :0.000                  Median :0.0000                       
##  Mean   :0.035                  Mean   :0.4444                       
##  3rd Qu.:0.000                  3rd Qu.:1.0000                       
##  Max.   :1.000                  Max.   :1.0000                       
##  NA's   :719                    NA's   :695                          
##  Day15cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp Day15cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp
##  Min.   :0.0000                        Min.   :0.0000                         
##  1st Qu.:0.0000                        1st Qu.:0.0000                         
##  Median :0.0000                        Median :0.0000                         
##  Mean   :0.2326                        Mean   :0.4661                         
##  3rd Qu.:0.0000                        3rd Qu.:1.0000                         
##  Max.   :1.0000                        Max.   :1.0000                         
##  NA's   :703                           NA's   :687                            
##  Day15cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp Day15cd8_IFNg.IL2.TNFa_Wuhan.N_resp
##  Min.   :0.0000                          Min.   :0.0000                     
##  1st Qu.:0.0000                          1st Qu.:0.0000                     
##  Median :0.0000                          Median :0.0000                     
##  Mean   :0.2101                          Mean   :0.0276                     
##  3rd Qu.:0.0000                          3rd Qu.:0.0000                     
##  Max.   :1.0000                          Max.   :1.0000                     
##  NA's   :686                             NA's   :719                        
##  Day15cd8_IL2_BA.4.5.S1_resp Day15cd8_IL2_BA.4.5.S2_resp
##  Min.   :0.0000              Min.   :0.0000             
##  1st Qu.:0.0000              1st Qu.:0.0000             
##  Median :0.0000              Median :0.0000             
##  Mean   :0.1464              Mean   :0.0286             
##  3rd Qu.:0.0000              3rd Qu.:0.0000             
##  Max.   :1.0000              Max.   :1.0000             
##  NA's   :695                 NA's   :703                
##  Day15cd8_IL2_COV2.CON.S1_resp Day15cd8_IL2_COV2.CON.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :0.0000               
##  Mean   :0.1374                Mean   :0.0365               
##  3rd Qu.:0.0000                3rd Qu.:0.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :687                   NA's   :686                  
##  Day15cd8_IL2_Wuhan.N_resp Day15cd8_TNFa_BA.4.5.S1_resp
##  Min.   :0.0000            Min.   :0.0000              
##  1st Qu.:0.0000            1st Qu.:0.0000              
##  Median :0.0000            Median :0.0000              
##  Mean   :0.0055            Mean   :0.3474              
##  3rd Qu.:0.0000            3rd Qu.:1.0000              
##  Max.   :1.0000            Max.   :1.0000              
##  NA's   :719               NA's   :695                 
##  Day15cd8_TNFa_BA.4.5.S2_resp Day15cd8_TNFa_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :0.0000               Median :0.0000                
##  Mean   :0.1646               Mean   :0.3478                
##  3rd Qu.:0.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :703                  NA's   :687                   
##  Day15cd8_TNFa_COV2.CON.S2_resp Day15cd8_TNFa_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:0.0000                 1st Qu.:0.0000            
##  Median :0.0000                 Median :0.0000            
##  Mean   :0.1372                 Mean   :0.0074            
##  3rd Qu.:0.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :686                    NA's   :719               
##  Day91cd4_154_BA.4.5.S1_resp Day91cd4_154_BA.4.5.S2_resp
##  Min.   :0.0000              Min.   :0.000              
##  1st Qu.:0.0000              1st Qu.:0.000              
##  Median :1.0000              Median :1.000              
##  Mean   :0.6529              Mean   :0.744              
##  3rd Qu.:1.0000              3rd Qu.:1.000              
##  Max.   :1.0000              Max.   :1.000              
##  NA's   :1092                NA's   :1094               
##  Day91cd4_154_COV2.CON.S1_resp Day91cd4_154_COV2.CON.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:1.0000                1st Qu.:1.0000               
##  Median :1.0000                Median :1.0000               
##  Mean   :0.7989                Mean   :0.8046               
##  3rd Qu.:1.0000                3rd Qu.:1.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :1088                  NA's   :1088                 
##  Day91cd4_154_Wuhan.N_resp Day91cd4_CXCR5.154_BA.4.5.S1_resp
##  Min.   :0.0000            Min.   :0.0000                   
##  1st Qu.:0.0000            1st Qu.:0.0000                   
##  Median :0.0000            Median :0.0000                   
##  Mean   :0.1783            Mean   :0.0184                   
##  3rd Qu.:0.0000            3rd Qu.:0.0000                   
##  Max.   :1.0000            Max.   :1.0000                   
##  NA's   :1105              NA's   :1099                     
##  Day91cd4_CXCR5.154_BA.4.5.S2_resp Day91cd4_CXCR5.154_COV2.CON.S1_resp
##  Min.   :0.0000                    Min.   :0.000                      
##  1st Qu.:0.0000                    1st Qu.:0.000                      
##  Median :0.0000                    Median :0.000                      
##  Mean   :0.0181                    Mean   :0.023                      
##  3rd Qu.:0.0000                    3rd Qu.:0.000                      
##  Max.   :1.0000                    Max.   :1.000                      
##  NA's   :1096                      NA's   :1088                       
##  Day91cd4_CXCR5.154_COV2.CON.S2_resp Day91cd4_CXCR5.154_Wuhan.N_resp
##  Min.   :0.0000                      Min.   :0                      
##  1st Qu.:0.0000                      1st Qu.:0                      
##  Median :0.0000                      Median :0                      
##  Mean   :0.0172                      Mean   :0                      
##  3rd Qu.:0.0000                      3rd Qu.:0                      
##  Max.   :1.0000                      Max.   :0                      
##  NA's   :1088                        NA's   :1111                   
##  Day91cd4_CXCR5.IL21_BA.4.5.S1_resp Day91cd4_CXCR5.IL21_BA.4.5.S2_resp
##  Min.   :0                          Min.   :0                         
##  1st Qu.:0                          1st Qu.:0                         
##  Median :0                          Median :0                         
##  Mean   :0                          Mean   :0                         
##  3rd Qu.:0                          3rd Qu.:0                         
##  Max.   :0                          Max.   :0                         
##  NA's   :1099                       NA's   :1096                      
##  Day91cd4_CXCR5.IL21_COV2.CON.S1_resp Day91cd4_CXCR5.IL21_COV2.CON.S2_resp
##  Min.   :0                            Min.   :0                           
##  1st Qu.:0                            1st Qu.:0                           
##  Median :0                            Median :0                           
##  Mean   :0                            Mean   :0                           
##  3rd Qu.:0                            3rd Qu.:0                           
##  Max.   :0                            Max.   :0                           
##  NA's   :1088                         NA's   :1088                        
##  Day91cd4_CXCR5.IL21_Wuhan.N_resp Day91cd4_IFNg_BA.4.5.S1_resp
##  Min.   :0                        Min.   :0.0000              
##  1st Qu.:0                        1st Qu.:0.0000              
##  Median :0                        Median :1.0000              
##  Mean   :0                        Mean   :0.6235              
##  3rd Qu.:0                        3rd Qu.:1.0000              
##  Max.   :0                        Max.   :1.0000              
##  NA's   :1111                     NA's   :1092                
##  Day91cd4_IFNg_BA.4.5.S2_resp Day91cd4_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :1.0000               Median :1.0000                
##  Mean   :0.7143               Mean   :0.7414                
##  3rd Qu.:1.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :1094                 NA's   :1088                  
##  Day91cd4_IFNg_COV2.CON.S2_resp Day91cd4_IFNg_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:1.0000                 1st Qu.:0.0000            
##  Median :1.0000                 Median :0.0000            
##  Mean   :0.7529                 Mean   :0.1465            
##  3rd Qu.:1.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :1088                   NA's   :1105              
##  Day91cd4_IFNg.IL2_BA.4.5.S1_resp Day91cd4_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000                   Min.   :0.0000                  
##  1st Qu.:0.0000                   1st Qu.:0.0000                  
##  Median :1.0000                   Median :1.0000                  
##  Mean   :0.6353                   Mean   :0.7143                  
##  3rd Qu.:1.0000                   3rd Qu.:1.0000                  
##  Max.   :1.0000                   Max.   :1.0000                  
##  NA's   :1092                     NA's   :1094                    
##  Day91cd4_IFNg.IL2_COV2.CON.S1_resp Day91cd4_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:1.0000                     1st Qu.:1.0000                    
##  Median :1.0000                     Median :1.0000                    
##  Mean   :0.7644                     Mean   :0.7759                    
##  3rd Qu.:1.0000                     3rd Qu.:1.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :1088                       NA's   :1088                      
##  Day91cd4_IFNg.IL2_Wuhan.N_resp Day91cd4_IFNg.IL2.154_BA.4.5.S1_resp
##  Min.   :0.0000                 Min.   :0.0000                      
##  1st Qu.:0.0000                 1st Qu.:0.0000                      
##  Median :0.0000                 Median :1.0000                      
##  Mean   :0.1783                 Mean   :0.6294                      
##  3rd Qu.:0.0000                 3rd Qu.:1.0000                      
##  Max.   :1.0000                 Max.   :1.0000                      
##  NA's   :1105                   NA's   :1092                        
##  Day91cd4_IFNg.IL2.154_BA.4.5.S2_resp Day91cd4_IFNg.IL2.154_COV2.CON.S1_resp
##  Min.   :0.0000                       Min.   :0.0000                        
##  1st Qu.:0.0000                       1st Qu.:1.0000                        
##  Median :1.0000                       Median :1.0000                        
##  Mean   :0.6905                       Mean   :0.7644                        
##  3rd Qu.:1.0000                       3rd Qu.:1.0000                        
##  Max.   :1.0000                       Max.   :1.0000                        
##  NA's   :1094                         NA's   :1088                          
##  Day91cd4_IFNg.IL2.154_COV2.CON.S2_resp Day91cd4_IFNg.IL2.154_Wuhan.N_resp
##  Min.   :0.0000                         Min.   :0.0000                    
##  1st Qu.:1.0000                         1st Qu.:0.0000                    
##  Median :1.0000                         Median :0.0000                    
##  Mean   :0.7701                         Mean   :0.1656                    
##  3rd Qu.:1.0000                         3rd Qu.:0.0000                    
##  Max.   :1.0000                         Max.   :1.0000                    
##  NA's   :1088                           NA's   :1105                      
##  Day91cd4_IL17a_BA.4.5.S1_resp Day91cd4_IL17a_BA.4.5.S2_resp
##  Min.   :0                     Min.   :0                    
##  1st Qu.:0                     1st Qu.:0                    
##  Median :0                     Median :0                    
##  Mean   :0                     Mean   :0                    
##  3rd Qu.:0                     3rd Qu.:0                    
##  Max.   :0                     Max.   :0                    
##  NA's   :1092                  NA's   :1094                 
##  Day91cd4_IL17a_COV2.CON.S1_resp Day91cd4_IL17a_COV2.CON.S2_resp
##  Min.   :0                       Min.   :0                      
##  1st Qu.:0                       1st Qu.:0                      
##  Median :0                       Median :0                      
##  Mean   :0                       Mean   :0                      
##  3rd Qu.:0                       3rd Qu.:0                      
##  Max.   :0                       Max.   :0                      
##  NA's   :1088                    NA's   :1088                   
##  Day91cd4_IL17a_Wuhan.N_resp Day91cd4_IL2_BA.4.5.S1_resp
##  Min.   :0                   Min.   :0.0000             
##  1st Qu.:0                   1st Qu.:0.0000             
##  Median :0                   Median :1.0000             
##  Mean   :0                   Mean   :0.5176             
##  3rd Qu.:0                   3rd Qu.:1.0000             
##  Max.   :0                   Max.   :1.0000             
##  NA's   :1105                NA's   :1092               
##  Day91cd4_IL2_BA.4.5.S2_resp Day91cd4_IL2_COV2.CON.S1_resp
##  Min.   :0.0000              Min.   :0.0000               
##  1st Qu.:0.0000              1st Qu.:0.0000               
##  Median :1.0000              Median :1.0000               
##  Mean   :0.5952              Mean   :0.6379               
##  3rd Qu.:1.0000              3rd Qu.:1.0000               
##  Max.   :1.0000              Max.   :1.0000               
##  NA's   :1094                NA's   :1088                 
##  Day91cd4_IL2_COV2.CON.S2_resp Day91cd4_IL2_Wuhan.N_resp
##  Min.   :0.0000                Min.   :0.0000           
##  1st Qu.:0.0000                1st Qu.:0.0000           
##  Median :1.0000                Median :0.0000           
##  Mean   :0.6494                Mean   :0.1338           
##  3rd Qu.:1.0000                3rd Qu.:0.0000           
##  Max.   :1.0000                Max.   :1.0000           
##  NA's   :1088                  NA's   :1105             
##  Day91cd4_IL21_BA.4.5.S1_resp Day91cd4_IL21_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :0.0000               Median :0.0000              
##  Mean   :0.0176               Mean   :0.0119              
##  3rd Qu.:0.0000               3rd Qu.:0.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :1092                 NA's   :1094                
##  Day91cd4_IL21_COV2.CON.S1_resp Day91cd4_IL21_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :0.0000                 Median :0.0000                
##  Mean   :0.0172                 Mean   :0.0172                
##  3rd Qu.:0.0000                 3rd Qu.:0.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :1088                   NA's   :1088                  
##  Day91cd4_IL21_Wuhan.N_resp Day91cd4_IL4.154_BA.4.5.S1_resp
##  Min.   :0                  Min.   :0.0000                 
##  1st Qu.:0                  1st Qu.:0.0000                 
##  Median :0                  Median :0.0000                 
##  Mean   :0                  Mean   :0.0059                 
##  3rd Qu.:0                  3rd Qu.:0.0000                 
##  Max.   :0                  Max.   :1.0000                 
##  NA's   :1105               NA's   :1092                   
##  Day91cd4_IL4.154_BA.4.5.S2_resp Day91cd4_IL4.154_COV2.CON.S1_resp
##  Min.   :0                       Min.   :0                        
##  1st Qu.:0                       1st Qu.:0                        
##  Median :0                       Median :0                        
##  Mean   :0                       Mean   :0                        
##  3rd Qu.:0                       3rd Qu.:0                        
##  Max.   :0                       Max.   :0                        
##  NA's   :1094                    NA's   :1088                     
##  Day91cd4_IL4.154_COV2.CON.S2_resp Day91cd4_IL4.154_Wuhan.N_resp
##  Min.   :0                         Min.   :0                    
##  1st Qu.:0                         1st Qu.:0                    
##  Median :0                         Median :0                    
##  Mean   :0                         Mean   :0                    
##  3rd Qu.:0                         3rd Qu.:0                    
##  Max.   :0                         Max.   :0                    
##  NA's   :1088                      NA's   :1105                 
##  Day91cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0.0000                          
##  1st Qu.:0.0000                          
##  Median :0.0000                          
##  Mean   :0.0059                          
##  3rd Qu.:0.0000                          
##  Max.   :1.0000                          
##  NA's   :1092                            
##  Day91cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp
##  Min.   :0                               
##  1st Qu.:0                               
##  Median :0                               
##  Mean   :0                               
##  3rd Qu.:0                               
##  Max.   :0                               
##  NA's   :1094                            
##  Day91cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0.0000                            
##  1st Qu.:0.0000                            
##  Median :0.0000                            
##  Mean   :0.0115                            
##  3rd Qu.:0.0000                            
##  Max.   :1.0000                            
##  NA's   :1088                              
##  Day91cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp
##  Min.   :0.0000                            
##  1st Qu.:0.0000                            
##  Median :0.0000                            
##  Mean   :0.0115                            
##  3rd Qu.:0.0000                            
##  Max.   :1.0000                            
##  NA's   :1088                              
##  Day91cd4_IL4.IL5.IL13.154_Wuhan.N_resp Day91cd4_IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0                              Min.   :0.0000                      
##  1st Qu.:0                              1st Qu.:0.0000                      
##  Median :0                              Median :0.0000                      
##  Mean   :0                              Mean   :0.0059                      
##  3rd Qu.:0                              3rd Qu.:0.0000                      
##  Max.   :0                              Max.   :1.0000                      
##  NA's   :1105                           NA's   :1092                        
##  Day91cd4_IL5.IL13.154_BA.4.5.S2_resp Day91cd4_IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0                            Min.   :0                             
##  1st Qu.:0                            1st Qu.:0                             
##  Median :0                            Median :0                             
##  Mean   :0                            Mean   :0                             
##  3rd Qu.:0                            3rd Qu.:0                             
##  Max.   :0                            Max.   :0                             
##  NA's   :1094                         NA's   :1088                          
##  Day91cd4_IL5.IL13.154_COV2.CON.S2_resp Day91cd4_IL5.IL13.154_Wuhan.N_resp
##  Min.   :0                              Min.   :0                         
##  1st Qu.:0                              1st Qu.:0                         
##  Median :0                              Median :0                         
##  Mean   :0                              Mean   :0                         
##  3rd Qu.:0                              3rd Qu.:0                         
##  Max.   :0                              Max.   :0                         
##  NA's   :1088                           NA's   :1105                      
##  Day91cd4_TNFa_BA.4.5.S1_resp Day91cd4_TNFa_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :0.0000               Median :1.0000              
##  Mean   :0.3765               Mean   :0.5298              
##  3rd Qu.:1.0000               3rd Qu.:1.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :1092                 NA's   :1094                
##  Day91cd4_TNFa_COV2.CON.S1_resp Day91cd4_TNFa_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :0.0000                 Median :1.0000                
##  Mean   :0.4425                 Mean   :0.5115                
##  3rd Qu.:1.0000                 3rd Qu.:1.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :1088                   NA's   :1088                  
##  Day91cd4_TNFa_Wuhan.N_resp Day91cd8_IFNg_BA.4.5.S1_resp
##  Min.   :0.0000             Min.   :0.0000              
##  1st Qu.:0.0000             1st Qu.:0.0000              
##  Median :0.0000             Median :0.0000              
##  Mean   :0.0318             Mean   :0.4793              
##  3rd Qu.:0.0000             3rd Qu.:1.0000              
##  Max.   :1.0000             Max.   :1.0000              
##  NA's   :1105               NA's   :1093                
##  Day91cd8_IFNg_BA.4.5.S2_resp Day91cd8_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :0.0000               Median :1.0000                
##  Mean   :0.2143               Mean   :0.5402                
##  3rd Qu.:0.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :1094                 NA's   :1088                  
##  Day91cd8_IFNg_COV2.CON.S2_resp Day91cd8_IFNg_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:0.0000                 1st Qu.:0.0000            
##  Median :0.0000                 Median :0.0000            
##  Mean   :0.2069                 Mean   :0.0255            
##  3rd Qu.:0.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :1088                   NA's   :1105              
##  Day91cd8_IFNg.IL2_BA.4.5.S1_resp Day91cd8_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000                   Min.   :0.0000                  
##  1st Qu.:0.0000                   1st Qu.:0.0000                  
##  Median :0.0000                   Median :0.0000                  
##  Mean   :0.4734                   Mean   :0.2143                  
##  3rd Qu.:1.0000                   3rd Qu.:0.0000                  
##  Max.   :1.0000                   Max.   :1.0000                  
##  NA's   :1093                     NA's   :1094                    
##  Day91cd8_IFNg.IL2_COV2.CON.S1_resp Day91cd8_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                     Min.   :0.0000                    
##  1st Qu.:0.0000                     1st Qu.:0.0000                    
##  Median :1.0000                     Median :0.0000                    
##  Mean   :0.5517                     Mean   :0.2011                    
##  3rd Qu.:1.0000                     3rd Qu.:0.0000                    
##  Max.   :1.0000                     Max.   :1.0000                    
##  NA's   :1088                       NA's   :1088                      
##  Day91cd8_IFNg.IL2_Wuhan.N_resp Day91cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp
##  Min.   :0.0000                 Min.   :0.0000                       
##  1st Qu.:0.0000                 1st Qu.:0.0000                       
##  Median :0.0000                 Median :0.0000                       
##  Mean   :0.0191                 Mean   :0.4675                       
##  3rd Qu.:0.0000                 3rd Qu.:1.0000                       
##  Max.   :1.0000                 Max.   :1.0000                       
##  NA's   :1105                   NA's   :1093                         
##  Day91cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp Day91cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp
##  Min.   :0.0000                        Min.   :0.0000                         
##  1st Qu.:0.0000                        1st Qu.:0.0000                         
##  Median :0.0000                        Median :1.0000                         
##  Mean   :0.1786                        Mean   :0.5115                         
##  3rd Qu.:0.0000                        3rd Qu.:1.0000                         
##  Max.   :1.0000                        Max.   :1.0000                         
##  NA's   :1094                          NA's   :1088                           
##  Day91cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp Day91cd8_IFNg.IL2.TNFa_Wuhan.N_resp
##  Min.   :0.0000                          Min.   :0.0000                     
##  1st Qu.:0.0000                          1st Qu.:0.0000                     
##  Median :0.0000                          Median :0.0000                     
##  Mean   :0.1782                          Mean   :0.0255                     
##  3rd Qu.:0.0000                          3rd Qu.:0.0000                     
##  Max.   :1.0000                          Max.   :1.0000                     
##  NA's   :1088                            NA's   :1105                       
##  Day91cd8_IL2_BA.4.5.S1_resp Day91cd8_IL2_BA.4.5.S2_resp
##  Min.   :0.0000              Min.   :0.0000             
##  1st Qu.:0.0000              1st Qu.:0.0000             
##  Median :0.0000              Median :0.0000             
##  Mean   :0.1893              Mean   :0.0119             
##  3rd Qu.:0.0000              3rd Qu.:0.0000             
##  Max.   :1.0000              Max.   :1.0000             
##  NA's   :1093                NA's   :1094               
##  Day91cd8_IL2_COV2.CON.S1_resp Day91cd8_IL2_COV2.CON.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :0.0000               
##  Mean   :0.1494                Mean   :0.0115               
##  3rd Qu.:0.0000                3rd Qu.:0.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :1088                  NA's   :1088                 
##  Day91cd8_IL2_Wuhan.N_resp Day91cd8_TNFa_BA.4.5.S1_resp
##  Min.   :0.0000            Min.   :0.0000              
##  1st Qu.:0.0000            1st Qu.:0.0000              
##  Median :0.0000            Median :0.0000              
##  Mean   :0.0127            Mean   :0.4379              
##  3rd Qu.:0.0000            3rd Qu.:1.0000              
##  Max.   :1.0000            Max.   :1.0000              
##  NA's   :1105              NA's   :1093                
##  Day91cd8_TNFa_BA.4.5.S2_resp Day91cd8_TNFa_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :0.0000               Median :0.0000                
##  Mean   :0.1429               Mean   :0.4195                
##  3rd Qu.:0.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :1094                 NA's   :1088                  
##  Day91cd8_TNFa_COV2.CON.S2_resp Day91cd8_TNFa_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.0000            
##  1st Qu.:0.0000                 1st Qu.:0.0000            
##  Median :0.0000                 Median :0.0000            
##  Mean   :0.1322                 Mean   :0.0064            
##  3rd Qu.:0.0000                 3rd Qu.:0.0000            
##  Max.   :1.0000                 Max.   :1.0000            
##  NA's   :1088                   NA's   :1105              
##  Day181cd4_154_BA.4.5.S1_resp Day181cd4_154_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :1.0000               Median :1.0000              
##  Mean   :0.6343               Mean   :0.7252              
##  3rd Qu.:1.0000               3rd Qu.:1.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :1128                 NA's   :1131                
##  Day181cd4_154_COV2.CON.S1_resp Day181cd4_154_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.000                 
##  1st Qu.:1.0000                 1st Qu.:1.000                 
##  Median :1.0000                 Median :1.000                 
##  Mean   :0.7554                 Mean   :0.777                 
##  3rd Qu.:1.0000                 3rd Qu.:1.000                 
##  Max.   :1.0000                 Max.   :1.000                 
##  NA's   :1123                   NA's   :1123                  
##  Day181cd4_154_Wuhan.N_resp Day181cd4_CXCR5.154_BA.4.5.S1_resp
##  Min.   :0.000              Min.   :0.0000                    
##  1st Qu.:0.000              1st Qu.:0.0000                    
##  Median :0.000              Median :0.0000                    
##  Mean   :0.192              Mean   :0.0075                    
##  3rd Qu.:0.000              3rd Qu.:0.0000                    
##  Max.   :1.000              Max.   :1.0000                    
##  NA's   :1137               NA's   :1128                      
##  Day181cd4_CXCR5.154_BA.4.5.S2_resp Day181cd4_CXCR5.154_COV2.CON.S1_resp
##  Min.   :0                          Min.   :0                           
##  1st Qu.:0                          1st Qu.:0                           
##  Median :0                          Median :0                           
##  Mean   :0                          Mean   :0                           
##  3rd Qu.:0                          3rd Qu.:0                           
##  Max.   :0                          Max.   :0                           
##  NA's   :1131                       NA's   :1123                        
##  Day181cd4_CXCR5.154_COV2.CON.S2_resp Day181cd4_CXCR5.154_Wuhan.N_resp
##  Min.   :0                            Min.   :0                       
##  1st Qu.:0                            1st Qu.:0                       
##  Median :0                            Median :0                       
##  Mean   :0                            Mean   :0                       
##  3rd Qu.:0                            3rd Qu.:0                       
##  Max.   :0                            Max.   :0                       
##  NA's   :1123                         NA's   :1143                    
##  Day181cd4_CXCR5.IL21_BA.4.5.S1_resp Day181cd4_CXCR5.IL21_BA.4.5.S2_resp
##  Min.   :0                           Min.   :0                          
##  1st Qu.:0                           1st Qu.:0                          
##  Median :0                           Median :0                          
##  Mean   :0                           Mean   :0                          
##  3rd Qu.:0                           3rd Qu.:0                          
##  Max.   :0                           Max.   :0                          
##  NA's   :1128                        NA's   :1131                       
##  Day181cd4_CXCR5.IL21_COV2.CON.S1_resp Day181cd4_CXCR5.IL21_COV2.CON.S2_resp
##  Min.   :0                             Min.   :0                            
##  1st Qu.:0                             1st Qu.:0                            
##  Median :0                             Median :0                            
##  Mean   :0                             Mean   :0                            
##  3rd Qu.:0                             3rd Qu.:0                            
##  Max.   :0                             Max.   :0                            
##  NA's   :1123                          NA's   :1123                         
##  Day181cd4_CXCR5.IL21_Wuhan.N_resp Day181cd4_IFNg_BA.4.5.S1_resp
##  Min.   :0                         Min.   :0.0000               
##  1st Qu.:0                         1st Qu.:0.0000               
##  Median :0                         Median :1.0000               
##  Mean   :0                         Mean   :0.5896               
##  3rd Qu.:0                         3rd Qu.:1.0000               
##  Max.   :0                         Max.   :1.0000               
##  NA's   :1143                      NA's   :1128                 
##  Day181cd4_IFNg_BA.4.5.S2_resp Day181cd4_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000                Min.   :0.000                  
##  1st Qu.:0.0000                1st Qu.:0.000                  
##  Median :1.0000                Median :1.000                  
##  Mean   :0.7328                Mean   :0.705                  
##  3rd Qu.:1.0000                3rd Qu.:1.000                  
##  Max.   :1.0000                Max.   :1.000                  
##  NA's   :1131                  NA's   :1123                   
##  Day181cd4_IFNg_COV2.CON.S2_resp Day181cd4_IFNg_Wuhan.N_resp
##  Min.   :0.0000                  Min.   :0.000              
##  1st Qu.:1.0000                  1st Qu.:0.000              
##  Median :1.0000                  Median :0.000              
##  Mean   :0.7626                  Mean   :0.216              
##  3rd Qu.:1.0000                  3rd Qu.:0.000              
##  Max.   :1.0000                  Max.   :1.000              
##  NA's   :1123                    NA's   :1137               
##  Day181cd4_IFNg.IL2_BA.4.5.S1_resp Day181cd4_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000                    Min.   :0.0000                   
##  1st Qu.:0.0000                    1st Qu.:0.0000                   
##  Median :1.0000                    Median :1.0000                   
##  Mean   :0.6343                    Mean   :0.7405                   
##  3rd Qu.:1.0000                    3rd Qu.:1.0000                   
##  Max.   :1.0000                    Max.   :1.0000                   
##  NA's   :1128                      NA's   :1131                     
##  Day181cd4_IFNg.IL2_COV2.CON.S1_resp Day181cd4_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                      Min.   :0.0000                     
##  1st Qu.:0.0000                      1st Qu.:1.0000                     
##  Median :1.0000                      Median :1.0000                     
##  Mean   :0.6906                      Mean   :0.7554                     
##  3rd Qu.:1.0000                      3rd Qu.:1.0000                     
##  Max.   :1.0000                      Max.   :1.0000                     
##  NA's   :1123                        NA's   :1123                       
##  Day181cd4_IFNg.IL2_Wuhan.N_resp Day181cd4_IFNg.IL2.154_BA.4.5.S1_resp
##  Min.   :0.000                   Min.   :0.0000                       
##  1st Qu.:0.000                   1st Qu.:0.0000                       
##  Median :0.000                   Median :1.0000                       
##  Mean   :0.224                   Mean   :0.6119                       
##  3rd Qu.:0.000                   3rd Qu.:1.0000                       
##  Max.   :1.000                   Max.   :1.0000                       
##  NA's   :1137                    NA's   :1128                         
##  Day181cd4_IFNg.IL2.154_BA.4.5.S2_resp Day181cd4_IFNg.IL2.154_COV2.CON.S1_resp
##  Min.   :0.0000                        Min.   :0.0000                         
##  1st Qu.:0.0000                        1st Qu.:0.0000                         
##  Median :1.0000                        Median :1.0000                         
##  Mean   :0.7252                        Mean   :0.7122                         
##  3rd Qu.:1.0000                        3rd Qu.:1.0000                         
##  Max.   :1.0000                        Max.   :1.0000                         
##  NA's   :1131                          NA's   :1123                           
##  Day181cd4_IFNg.IL2.154_COV2.CON.S2_resp Day181cd4_IFNg.IL2.154_Wuhan.N_resp
##  Min.   :0.0000                          Min.   :0.000                      
##  1st Qu.:0.0000                          1st Qu.:0.000                      
##  Median :1.0000                          Median :0.000                      
##  Mean   :0.7266                          Mean   :0.208                      
##  3rd Qu.:1.0000                          3rd Qu.:0.000                      
##  Max.   :1.0000                          Max.   :1.000                      
##  NA's   :1123                            NA's   :1137                       
##  Day181cd4_IL17a_BA.4.5.S1_resp Day181cd4_IL17a_BA.4.5.S2_resp
##  Min.   :0                      Min.   :0                     
##  1st Qu.:0                      1st Qu.:0                     
##  Median :0                      Median :0                     
##  Mean   :0                      Mean   :0                     
##  3rd Qu.:0                      3rd Qu.:0                     
##  Max.   :0                      Max.   :0                     
##  NA's   :1128                   NA's   :1131                  
##  Day181cd4_IL17a_COV2.CON.S1_resp Day181cd4_IL17a_COV2.CON.S2_resp
##  Min.   :0                        Min.   :0                       
##  1st Qu.:0                        1st Qu.:0                       
##  Median :0                        Median :0                       
##  Mean   :0                        Mean   :0                       
##  3rd Qu.:0                        3rd Qu.:0                       
##  Max.   :0                        Max.   :0                       
##  NA's   :1123                     NA's   :1123                    
##  Day181cd4_IL17a_Wuhan.N_resp Day181cd4_IL2_BA.4.5.S1_resp
##  Min.   :0                    Min.   :0.0000              
##  1st Qu.:0                    1st Qu.:0.0000              
##  Median :0                    Median :0.0000              
##  Mean   :0                    Mean   :0.4776              
##  3rd Qu.:0                    3rd Qu.:1.0000              
##  Max.   :0                    Max.   :1.0000              
##  NA's   :1137                 NA's   :1128                
##  Day181cd4_IL2_BA.4.5.S2_resp Day181cd4_IL2_COV2.CON.S1_resp
##  Min.   :0.0000               Min.   :0.0000                
##  1st Qu.:0.0000               1st Qu.:0.0000                
##  Median :1.0000               Median :1.0000                
##  Mean   :0.6183               Mean   :0.5971                
##  3rd Qu.:1.0000               3rd Qu.:1.0000                
##  Max.   :1.0000               Max.   :1.0000                
##  NA's   :1131                 NA's   :1123                  
##  Day181cd4_IL2_COV2.CON.S2_resp Day181cd4_IL2_Wuhan.N_resp
##  Min.   :0.0000                 Min.   :0.00              
##  1st Qu.:0.0000                 1st Qu.:0.00              
##  Median :1.0000                 Median :0.00              
##  Mean   :0.6259                 Mean   :0.16              
##  3rd Qu.:1.0000                 3rd Qu.:0.00              
##  Max.   :1.0000                 Max.   :1.00              
##  NA's   :1123                   NA's   :1137              
##  Day181cd4_IL21_BA.4.5.S1_resp Day181cd4_IL21_BA.4.5.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :0.0000               
##  Mean   :0.0224                Mean   :0.0153               
##  3rd Qu.:0.0000                3rd Qu.:0.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :1128                  NA's   :1131                 
##  Day181cd4_IL21_COV2.CON.S1_resp Day181cd4_IL21_COV2.CON.S2_resp
##  Min.   :0.0000                  Min.   :0.000                  
##  1st Qu.:0.0000                  1st Qu.:0.000                  
##  Median :0.0000                  Median :0.000                  
##  Mean   :0.0288                  Mean   :0.036                  
##  3rd Qu.:0.0000                  3rd Qu.:0.000                  
##  Max.   :1.0000                  Max.   :1.000                  
##  NA's   :1123                    NA's   :1123                   
##  Day181cd4_IL21_Wuhan.N_resp Day181cd4_IL4.154_BA.4.5.S1_resp
##  Min.   :0                   Min.   :0                       
##  1st Qu.:0                   1st Qu.:0                       
##  Median :0                   Median :0                       
##  Mean   :0                   Mean   :0                       
##  3rd Qu.:0                   3rd Qu.:0                       
##  Max.   :0                   Max.   :0                       
##  NA's   :1137                NA's   :1128                    
##  Day181cd4_IL4.154_BA.4.5.S2_resp Day181cd4_IL4.154_COV2.CON.S1_resp
##  Min.   :0                        Min.   :0                         
##  1st Qu.:0                        1st Qu.:0                         
##  Median :0                        Median :0                         
##  Mean   :0                        Mean   :0                         
##  3rd Qu.:0                        3rd Qu.:0                         
##  Max.   :0                        Max.   :0                         
##  NA's   :1131                     NA's   :1123                      
##  Day181cd4_IL4.154_COV2.CON.S2_resp Day181cd4_IL4.154_Wuhan.N_resp
##  Min.   :0.0000                     Min.   :0                     
##  1st Qu.:0.0000                     1st Qu.:0                     
##  Median :0.0000                     Median :0                     
##  Mean   :0.0072                     Mean   :0                     
##  3rd Qu.:0.0000                     3rd Qu.:0                     
##  Max.   :1.0000                     Max.   :0                     
##  NA's   :1123                       NA's   :1137                  
##  Day181cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0                                
##  1st Qu.:0                                
##  Median :0                                
##  Mean   :0                                
##  3rd Qu.:0                                
##  Max.   :0                                
##  NA's   :1128                             
##  Day181cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp
##  Min.   :0                                
##  1st Qu.:0                                
##  Median :0                                
##  Mean   :0                                
##  3rd Qu.:0                                
##  Max.   :0                                
##  NA's   :1131                             
##  Day181cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0                                  
##  1st Qu.:0                                  
##  Median :0                                  
##  Mean   :0                                  
##  3rd Qu.:0                                  
##  Max.   :0                                  
##  NA's   :1123                               
##  Day181cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp
##  Min.   :0.0000                             
##  1st Qu.:0.0000                             
##  Median :0.0000                             
##  Mean   :0.0144                             
##  3rd Qu.:0.0000                             
##  Max.   :1.0000                             
##  NA's   :1123                               
##  Day181cd4_IL4.IL5.IL13.154_Wuhan.N_resp Day181cd4_IL5.IL13.154_BA.4.5.S1_resp
##  Min.   :0                               Min.   :0                            
##  1st Qu.:0                               1st Qu.:0                            
##  Median :0                               Median :0                            
##  Mean   :0                               Mean   :0                            
##  3rd Qu.:0                               3rd Qu.:0                            
##  Max.   :0                               Max.   :0                            
##  NA's   :1137                            NA's   :1128                         
##  Day181cd4_IL5.IL13.154_BA.4.5.S2_resp Day181cd4_IL5.IL13.154_COV2.CON.S1_resp
##  Min.   :0                             Min.   :0                              
##  1st Qu.:0                             1st Qu.:0                              
##  Median :0                             Median :0                              
##  Mean   :0                             Mean   :0                              
##  3rd Qu.:0                             3rd Qu.:0                              
##  Max.   :0                             Max.   :0                              
##  NA's   :1131                          NA's   :1123                           
##  Day181cd4_IL5.IL13.154_COV2.CON.S2_resp Day181cd4_IL5.IL13.154_Wuhan.N_resp
##  Min.   :0.0000                          Min.   :0                          
##  1st Qu.:0.0000                          1st Qu.:0                          
##  Median :0.0000                          Median :0                          
##  Mean   :0.0072                          Mean   :0                          
##  3rd Qu.:0.0000                          3rd Qu.:0                          
##  Max.   :1.0000                          Max.   :0                          
##  NA's   :1123                            NA's   :1137                       
##  Day181cd4_TNFa_BA.4.5.S1_resp Day181cd4_TNFa_BA.4.5.S2_resp
##  Min.   :0.0000                Min.   :0.0000               
##  1st Qu.:0.0000                1st Qu.:0.0000               
##  Median :0.0000                Median :1.0000               
##  Mean   :0.3731                Mean   :0.5038               
##  3rd Qu.:1.0000                3rd Qu.:1.0000               
##  Max.   :1.0000                Max.   :1.0000               
##  NA's   :1128                  NA's   :1131                 
##  Day181cd4_TNFa_COV2.CON.S1_resp Day181cd4_TNFa_COV2.CON.S2_resp
##  Min.   :0.0000                  Min.   :0.0000                 
##  1st Qu.:0.0000                  1st Qu.:0.0000                 
##  Median :0.0000                  Median :0.0000                 
##  Mean   :0.3957                  Mean   :0.4964                 
##  3rd Qu.:1.0000                  3rd Qu.:1.0000                 
##  Max.   :1.0000                  Max.   :1.0000                 
##  NA's   :1123                    NA's   :1123                   
##  Day181cd4_TNFa_Wuhan.N_resp Day181cd8_IFNg_BA.4.5.S1_resp
##  Min.   :0.000               Min.   :0.0000               
##  1st Qu.:0.000               1st Qu.:0.0000               
##  Median :0.000               Median :0.0000               
##  Mean   :0.088               Mean   :0.4586               
##  3rd Qu.:0.000               3rd Qu.:1.0000               
##  Max.   :1.000               Max.   :1.0000               
##  NA's   :1137                NA's   :1129                 
##  Day181cd8_IFNg_BA.4.5.S2_resp Day181cd8_IFNg_COV2.CON.S1_resp
##  Min.   :0.0000                Min.   :0.0000                 
##  1st Qu.:0.0000                1st Qu.:0.0000                 
##  Median :0.0000                Median :1.0000                 
##  Mean   :0.1679                Mean   :0.5036                 
##  3rd Qu.:0.0000                3rd Qu.:1.0000                 
##  Max.   :1.0000                Max.   :1.0000                 
##  NA's   :1131                  NA's   :1123                   
##  Day181cd8_IFNg_COV2.CON.S2_resp Day181cd8_IFNg_Wuhan.N_resp
##  Min.   :0.0000                  Min.   :0.000              
##  1st Qu.:0.0000                  1st Qu.:0.000              
##  Median :0.0000                  Median :0.000              
##  Mean   :0.2014                  Mean   :0.064              
##  3rd Qu.:0.0000                  3rd Qu.:0.000              
##  Max.   :1.0000                  Max.   :1.000              
##  NA's   :1123                    NA's   :1137               
##  Day181cd8_IFNg.IL2_BA.4.5.S1_resp Day181cd8_IFNg.IL2_BA.4.5.S2_resp
##  Min.   :0.0000                    Min.   :0.0000                   
##  1st Qu.:0.0000                    1st Qu.:0.0000                   
##  Median :0.0000                    Median :0.0000                   
##  Mean   :0.4511                    Mean   :0.1679                   
##  3rd Qu.:1.0000                    3rd Qu.:0.0000                   
##  Max.   :1.0000                    Max.   :1.0000                   
##  NA's   :1129                      NA's   :1131                     
##  Day181cd8_IFNg.IL2_COV2.CON.S1_resp Day181cd8_IFNg.IL2_COV2.CON.S2_resp
##  Min.   :0.0000                      Min.   :0.0000                     
##  1st Qu.:0.0000                      1st Qu.:0.0000                     
##  Median :0.0000                      Median :0.0000                     
##  Mean   :0.4892                      Mean   :0.1799                     
##  3rd Qu.:1.0000                      3rd Qu.:0.0000                     
##  Max.   :1.0000                      Max.   :1.0000                     
##  NA's   :1123                        NA's   :1123                       
##  Day181cd8_IFNg.IL2_Wuhan.N_resp Day181cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp
##  Min.   :0.000                   Min.   :0.0000                        
##  1st Qu.:0.000                   1st Qu.:0.0000                        
##  Median :0.000                   Median :0.0000                        
##  Mean   :0.064                   Mean   :0.4511                        
##  3rd Qu.:0.000                   3rd Qu.:1.0000                        
##  Max.   :1.000                   Max.   :1.0000                        
##  NA's   :1137                    NA's   :1129                          
##  Day181cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp
##  Min.   :0.0000                        
##  1st Qu.:0.0000                        
##  Median :0.0000                        
##  Mean   :0.1527                        
##  3rd Qu.:0.0000                        
##  Max.   :1.0000                        
##  NA's   :1131                          
##  Day181cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp
##  Min.   :0.0000                          
##  1st Qu.:0.0000                          
##  Median :0.0000                          
##  Mean   :0.4748                          
##  3rd Qu.:1.0000                          
##  Max.   :1.0000                          
##  NA's   :1123                            
##  Day181cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp Day181cd8_IFNg.IL2.TNFa_Wuhan.N_resp
##  Min.   :0.0000                           Min.   :0.000                       
##  1st Qu.:0.0000                           1st Qu.:0.000                       
##  Median :0.0000                           Median :0.000                       
##  Mean   :0.1727                           Mean   :0.032                       
##  3rd Qu.:0.0000                           3rd Qu.:0.000                       
##  Max.   :1.0000                           Max.   :1.000                       
##  NA's   :1123                             NA's   :1137                        
##  Day181cd8_IL2_BA.4.5.S1_resp Day181cd8_IL2_BA.4.5.S2_resp
##  Min.   :0.0000               Min.   :0.0000              
##  1st Qu.:0.0000               1st Qu.:0.0000              
##  Median :0.0000               Median :0.0000              
##  Mean   :0.1278               Mean   :0.0076              
##  3rd Qu.:0.0000               3rd Qu.:0.0000              
##  Max.   :1.0000               Max.   :1.0000              
##  NA's   :1129                 NA's   :1131                
##  Day181cd8_IL2_COV2.CON.S1_resp Day181cd8_IL2_COV2.CON.S2_resp
##  Min.   :0.0000                 Min.   :0.0000                
##  1st Qu.:0.0000                 1st Qu.:0.0000                
##  Median :0.0000                 Median :0.0000                
##  Mean   :0.1367                 Mean   :0.0072                
##  3rd Qu.:0.0000                 3rd Qu.:0.0000                
##  Max.   :1.0000                 Max.   :1.0000                
##  NA's   :1123                   NA's   :1123                  
##  Day181cd8_IL2_Wuhan.N_resp Day181cd8_TNFa_BA.4.5.S1_resp
##  Min.   :0.000              Min.   :0.000                
##  1st Qu.:0.000              1st Qu.:0.000                
##  Median :0.000              Median :0.000                
##  Mean   :0.008              Mean   :0.406                
##  3rd Qu.:0.000              3rd Qu.:1.000                
##  Max.   :1.000              Max.   :1.000                
##  NA's   :1137               NA's   :1129                 
##  Day181cd8_TNFa_BA.4.5.S2_resp Day181cd8_TNFa_COV2.CON.S1_resp
##  Min.   :0.0000                Min.   :0.0000                 
##  1st Qu.:0.0000                1st Qu.:0.0000                 
##  Median :0.0000                Median :0.0000                 
##  Mean   :0.1298                Mean   :0.4317                 
##  3rd Qu.:0.0000                3rd Qu.:1.0000                 
##  Max.   :1.0000                Max.   :1.0000                 
##  NA's   :1131                  NA's   :1123                   
##  Day181cd8_TNFa_COV2.CON.S2_resp Day181cd8_TNFa_Wuhan.N_resp      ics       
##  Min.   :0.0000                  Min.   :0.000               Min.   :0.000  
##  1st Qu.:0.0000                  1st Qu.:0.000               1st Qu.:0.000  
##  Median :0.0000                  Median :0.000               Median :0.000  
##  Mean   :0.1583                  Mean   :0.008               Mean   :0.462  
##  3rd Qu.:0.0000                  3rd Qu.:0.000               3rd Qu.:1.000  
##  Max.   :1.0000                  Max.   :1.000               Max.   :1.000  
##  NA's   :1123                    NA's   :1137
sort(names(dat_mapped))
##   [1] "Actual_visit_date_1.0"                        
##   [2] "Actual_visit_date_15.2"                       
##   [3] "Actual_visit_date_181.14"                     
##   [4] "Actual_visit_date_271.14"                     
##   [5] "Actual_visit_date_29.2"                       
##   [6] "Actual_visit_date_91.7"                       
##   [7] "Age"                                          
##   [8] "Age65C"                                       
##   [9] "arm"                                          
##  [10] "Asian"                                        
##  [11] "ASSAY"                                        
##  [12] "ASSCOMP_SWAB1"                                
##  [13] "ASSCOMP_SWAB2"                                
##  [14] "ASSQC_SWAB1"                                  
##  [15] "ASSQC_SWAB2"                                  
##  [16] "ASSSTAT_SWAB1"                                
##  [17] "ASSSTAT_SWAB2"                                
##  [18] "AsympInfectIndD15to181"                       
##  [19] "AsympInfectIndD15to271"                       
##  [20] "AsympInfectIndD15to29"                        
##  [21] "AsympInfectIndD15to91"                        
##  [22] "AsympInfectIndD182to271"                      
##  [23] "AsympInfectIndD30to91"                        
##  [24] "AsympInfectIndD92to181"                       
##  [25] "BACRDPCT_SWAB1"                               
##  [26] "BACRDPCT_SWAB2"                               
##  [27] "Bcd4_154_BA.4.5.S1"                           
##  [28] "Bcd4_154_BA.4.5.S1_resp"                      
##  [29] "Bcd4_154_BA.4.5.S2"                           
##  [30] "Bcd4_154_BA.4.5.S2_resp"                      
##  [31] "Bcd4_154_COV2.CON.S1"                         
##  [32] "Bcd4_154_COV2.CON.S1_resp"                    
##  [33] "Bcd4_154_COV2.CON.S2"                         
##  [34] "Bcd4_154_COV2.CON.S2_resp"                    
##  [35] "Bcd4_154_Wuhan.N"                             
##  [36] "Bcd4_154_Wuhan.N_resp"                        
##  [37] "Bcd4_CXCR5.154_BA.4.5.S1"                     
##  [38] "Bcd4_CXCR5.154_BA.4.5.S1_resp"                
##  [39] "Bcd4_CXCR5.154_BA.4.5.S2"                     
##  [40] "Bcd4_CXCR5.154_BA.4.5.S2_resp"                
##  [41] "Bcd4_CXCR5.154_COV2.CON.S1"                   
##  [42] "Bcd4_CXCR5.154_COV2.CON.S1_resp"              
##  [43] "Bcd4_CXCR5.154_COV2.CON.S2"                   
##  [44] "Bcd4_CXCR5.154_COV2.CON.S2_resp"              
##  [45] "Bcd4_CXCR5.154_Wuhan.N"                       
##  [46] "Bcd4_CXCR5.154_Wuhan.N_resp"                  
##  [47] "Bcd4_CXCR5.IL21_BA.4.5.S1"                    
##  [48] "Bcd4_CXCR5.IL21_BA.4.5.S1_resp"               
##  [49] "Bcd4_CXCR5.IL21_BA.4.5.S2"                    
##  [50] "Bcd4_CXCR5.IL21_BA.4.5.S2_resp"               
##  [51] "Bcd4_CXCR5.IL21_COV2.CON.S1"                  
##  [52] "Bcd4_CXCR5.IL21_COV2.CON.S1_resp"             
##  [53] "Bcd4_CXCR5.IL21_COV2.CON.S2"                  
##  [54] "Bcd4_CXCR5.IL21_COV2.CON.S2_resp"             
##  [55] "Bcd4_CXCR5.IL21_Wuhan.N"                      
##  [56] "Bcd4_CXCR5.IL21_Wuhan.N_resp"                 
##  [57] "Bcd4_IFNg_BA.4.5.S1"                          
##  [58] "Bcd4_IFNg_BA.4.5.S1_resp"                     
##  [59] "Bcd4_IFNg_BA.4.5.S2"                          
##  [60] "Bcd4_IFNg_BA.4.5.S2_resp"                     
##  [61] "Bcd4_IFNg_COV2.CON.S1"                        
##  [62] "Bcd4_IFNg_COV2.CON.S1_resp"                   
##  [63] "Bcd4_IFNg_COV2.CON.S2"                        
##  [64] "Bcd4_IFNg_COV2.CON.S2_resp"                   
##  [65] "Bcd4_IFNg_Wuhan.N"                            
##  [66] "Bcd4_IFNg_Wuhan.N_resp"                       
##  [67] "Bcd4_IFNg.IL2_BA.4.5.S1"                      
##  [68] "Bcd4_IFNg.IL2_BA.4.5.S1_resp"                 
##  [69] "Bcd4_IFNg.IL2_BA.4.5.S2"                      
##  [70] "Bcd4_IFNg.IL2_BA.4.5.S2_resp"                 
##  [71] "Bcd4_IFNg.IL2_COV2.CON.S1"                    
##  [72] "Bcd4_IFNg.IL2_COV2.CON.S1_resp"               
##  [73] "Bcd4_IFNg.IL2_COV2.CON.S2"                    
##  [74] "Bcd4_IFNg.IL2_COV2.CON.S2_resp"               
##  [75] "Bcd4_IFNg.IL2_Wuhan.N"                        
##  [76] "Bcd4_IFNg.IL2_Wuhan.N_resp"                   
##  [77] "Bcd4_IFNg.IL2.154_BA.4.5.S1"                  
##  [78] "Bcd4_IFNg.IL2.154_BA.4.5.S1_resp"             
##  [79] "Bcd4_IFNg.IL2.154_BA.4.5.S2"                  
##  [80] "Bcd4_IFNg.IL2.154_BA.4.5.S2_resp"             
##  [81] "Bcd4_IFNg.IL2.154_COV2.CON.S1"                
##  [82] "Bcd4_IFNg.IL2.154_COV2.CON.S1_resp"           
##  [83] "Bcd4_IFNg.IL2.154_COV2.CON.S2"                
##  [84] "Bcd4_IFNg.IL2.154_COV2.CON.S2_resp"           
##  [85] "Bcd4_IFNg.IL2.154_Wuhan.N"                    
##  [86] "Bcd4_IFNg.IL2.154_Wuhan.N_resp"               
##  [87] "Bcd4_IL17a_BA.4.5.S1"                         
##  [88] "Bcd4_IL17a_BA.4.5.S1_resp"                    
##  [89] "Bcd4_IL17a_BA.4.5.S2"                         
##  [90] "Bcd4_IL17a_BA.4.5.S2_resp"                    
##  [91] "Bcd4_IL17a_COV2.CON.S1"                       
##  [92] "Bcd4_IL17a_COV2.CON.S1_resp"                  
##  [93] "Bcd4_IL17a_COV2.CON.S2"                       
##  [94] "Bcd4_IL17a_COV2.CON.S2_resp"                  
##  [95] "Bcd4_IL17a_Wuhan.N"                           
##  [96] "Bcd4_IL17a_Wuhan.N_resp"                      
##  [97] "Bcd4_IL2_BA.4.5.S1"                           
##  [98] "Bcd4_IL2_BA.4.5.S1_resp"                      
##  [99] "Bcd4_IL2_BA.4.5.S2"                           
## [100] "Bcd4_IL2_BA.4.5.S2_resp"                      
## [101] "Bcd4_IL2_COV2.CON.S1"                         
## [102] "Bcd4_IL2_COV2.CON.S1_resp"                    
## [103] "Bcd4_IL2_COV2.CON.S2"                         
## [104] "Bcd4_IL2_COV2.CON.S2_resp"                    
## [105] "Bcd4_IL2_Wuhan.N"                             
## [106] "Bcd4_IL2_Wuhan.N_resp"                        
## [107] "Bcd4_IL21_BA.4.5.S1"                          
## [108] "Bcd4_IL21_BA.4.5.S1_resp"                     
## [109] "Bcd4_IL21_BA.4.5.S2"                          
## [110] "Bcd4_IL21_BA.4.5.S2_resp"                     
## [111] "Bcd4_IL21_COV2.CON.S1"                        
## [112] "Bcd4_IL21_COV2.CON.S1_resp"                   
## [113] "Bcd4_IL21_COV2.CON.S2"                        
## [114] "Bcd4_IL21_COV2.CON.S2_resp"                   
## [115] "Bcd4_IL21_Wuhan.N"                            
## [116] "Bcd4_IL21_Wuhan.N_resp"                       
## [117] "Bcd4_IL4.154_BA.4.5.S1"                       
## [118] "Bcd4_IL4.154_BA.4.5.S1_resp"                  
## [119] "Bcd4_IL4.154_BA.4.5.S2"                       
## [120] "Bcd4_IL4.154_BA.4.5.S2_resp"                  
## [121] "Bcd4_IL4.154_COV2.CON.S1"                     
## [122] "Bcd4_IL4.154_COV2.CON.S1_resp"                
## [123] "Bcd4_IL4.154_COV2.CON.S2"                     
## [124] "Bcd4_IL4.154_COV2.CON.S2_resp"                
## [125] "Bcd4_IL4.154_Wuhan.N"                         
## [126] "Bcd4_IL4.154_Wuhan.N_resp"                    
## [127] "Bcd4_IL4.IL5.IL13.154_BA.4.5.S1"              
## [128] "Bcd4_IL4.IL5.IL13.154_BA.4.5.S1_resp"         
## [129] "Bcd4_IL4.IL5.IL13.154_BA.4.5.S2"              
## [130] "Bcd4_IL4.IL5.IL13.154_BA.4.5.S2_resp"         
## [131] "Bcd4_IL4.IL5.IL13.154_COV2.CON.S1"            
## [132] "Bcd4_IL4.IL5.IL13.154_COV2.CON.S1_resp"       
## [133] "Bcd4_IL4.IL5.IL13.154_COV2.CON.S2"            
## [134] "Bcd4_IL4.IL5.IL13.154_COV2.CON.S2_resp"       
## [135] "Bcd4_IL4.IL5.IL13.154_Wuhan.N"                
## [136] "Bcd4_IL4.IL5.IL13.154_Wuhan.N_resp"           
## [137] "Bcd4_IL5.IL13.154_BA.4.5.S1"                  
## [138] "Bcd4_IL5.IL13.154_BA.4.5.S1_resp"             
## [139] "Bcd4_IL5.IL13.154_BA.4.5.S2"                  
## [140] "Bcd4_IL5.IL13.154_BA.4.5.S2_resp"             
## [141] "Bcd4_IL5.IL13.154_COV2.CON.S1"                
## [142] "Bcd4_IL5.IL13.154_COV2.CON.S1_resp"           
## [143] "Bcd4_IL5.IL13.154_COV2.CON.S2"                
## [144] "Bcd4_IL5.IL13.154_COV2.CON.S2_resp"           
## [145] "Bcd4_IL5.IL13.154_Wuhan.N"                    
## [146] "Bcd4_IL5.IL13.154_Wuhan.N_resp"               
## [147] "Bcd4_TNFa_BA.4.5.S1"                          
## [148] "Bcd4_TNFa_BA.4.5.S1_resp"                     
## [149] "Bcd4_TNFa_BA.4.5.S2"                          
## [150] "Bcd4_TNFa_BA.4.5.S2_resp"                     
## [151] "Bcd4_TNFa_COV2.CON.S1"                        
## [152] "Bcd4_TNFa_COV2.CON.S1_resp"                   
## [153] "Bcd4_TNFa_COV2.CON.S2"                        
## [154] "Bcd4_TNFa_COV2.CON.S2_resp"                   
## [155] "Bcd4_TNFa_Wuhan.N"                            
## [156] "Bcd4_TNFa_Wuhan.N_resp"                       
## [157] "Bcd8_IFNg_BA.4.5.S1"                          
## [158] "Bcd8_IFNg_BA.4.5.S1_resp"                     
## [159] "Bcd8_IFNg_BA.4.5.S2"                          
## [160] "Bcd8_IFNg_BA.4.5.S2_resp"                     
## [161] "Bcd8_IFNg_COV2.CON.S1"                        
## [162] "Bcd8_IFNg_COV2.CON.S1_resp"                   
## [163] "Bcd8_IFNg_COV2.CON.S2"                        
## [164] "Bcd8_IFNg_COV2.CON.S2_resp"                   
## [165] "Bcd8_IFNg_Wuhan.N"                            
## [166] "Bcd8_IFNg_Wuhan.N_resp"                       
## [167] "Bcd8_IFNg.IL2_BA.4.5.S1"                      
## [168] "Bcd8_IFNg.IL2_BA.4.5.S1_resp"                 
## [169] "Bcd8_IFNg.IL2_BA.4.5.S2"                      
## [170] "Bcd8_IFNg.IL2_BA.4.5.S2_resp"                 
## [171] "Bcd8_IFNg.IL2_COV2.CON.S1"                    
## [172] "Bcd8_IFNg.IL2_COV2.CON.S1_resp"               
## [173] "Bcd8_IFNg.IL2_COV2.CON.S2"                    
## [174] "Bcd8_IFNg.IL2_COV2.CON.S2_resp"               
## [175] "Bcd8_IFNg.IL2_Wuhan.N"                        
## [176] "Bcd8_IFNg.IL2_Wuhan.N_resp"                   
## [177] "Bcd8_IFNg.IL2.TNFa_BA.4.5.S1"                 
## [178] "Bcd8_IFNg.IL2.TNFa_BA.4.5.S1_resp"            
## [179] "Bcd8_IFNg.IL2.TNFa_BA.4.5.S2"                 
## [180] "Bcd8_IFNg.IL2.TNFa_BA.4.5.S2_resp"            
## [181] "Bcd8_IFNg.IL2.TNFa_COV2.CON.S1"               
## [182] "Bcd8_IFNg.IL2.TNFa_COV2.CON.S1_resp"          
## [183] "Bcd8_IFNg.IL2.TNFa_COV2.CON.S2"               
## [184] "Bcd8_IFNg.IL2.TNFa_COV2.CON.S2_resp"          
## [185] "Bcd8_IFNg.IL2.TNFa_Wuhan.N"                   
## [186] "Bcd8_IFNg.IL2.TNFa_Wuhan.N_resp"              
## [187] "Bcd8_IL2_BA.4.5.S1"                           
## [188] "Bcd8_IL2_BA.4.5.S1_resp"                      
## [189] "Bcd8_IL2_BA.4.5.S2"                           
## [190] "Bcd8_IL2_BA.4.5.S2_resp"                      
## [191] "Bcd8_IL2_COV2.CON.S1"                         
## [192] "Bcd8_IL2_COV2.CON.S1_resp"                    
## [193] "Bcd8_IL2_COV2.CON.S2"                         
## [194] "Bcd8_IL2_COV2.CON.S2_resp"                    
## [195] "Bcd8_IL2_Wuhan.N"                             
## [196] "Bcd8_IL2_Wuhan.N_resp"                        
## [197] "Bcd8_TNFa_BA.4.5.S1"                          
## [198] "Bcd8_TNFa_BA.4.5.S1_resp"                     
## [199] "Bcd8_TNFa_BA.4.5.S2"                          
## [200] "Bcd8_TNFa_BA.4.5.S2_resp"                     
## [201] "Bcd8_TNFa_COV2.CON.S1"                        
## [202] "Bcd8_TNFa_COV2.CON.S1_resp"                   
## [203] "Bcd8_TNFa_COV2.CON.S2"                        
## [204] "Bcd8_TNFa_COV2.CON.S2_resp"                   
## [205] "Bcd8_TNFa_Wuhan.N"                            
## [206] "Bcd8_TNFa_Wuhan.N_resp"                       
## [207] "Black"                                        
## [208] "Bpseudoneutid50_BA.1"                         
## [209] "Bpseudoneutid50_BA.4.BA.5"                    
## [210] "Bpseudoneutid50_Beta"                         
## [211] "Bpseudoneutid50_D614G"                        
## [212] "Bpseudoneutid50_Delta"                        
## [213] "Bpseudoneutid50Duke_BA.2.12.1"                
## [214] "City"                                         
## [215] "CNSR_D22toD181"                               
## [216] "CNSR_D22toD91"                                
## [217] "CNSR_D22toend"                                
## [218] "CNSR_D36toD181"                               
## [219] "CNSR_D92toD181"                               
## [220] "CNSR1_D22toD181"                              
## [221] "CNSR1_D22toD91"                               
## [222] "CNSR1_D22toend"                               
## [223] "CNSR1_D36toD181"                              
## [224] "CNSR1_D92toD181"                              
## [225] "CNSR2"                                        
## [226] "CNSR3"                                        
## [227] "CNSR4"                                        
## [228] "CNSR5"                                        
## [229] "COVIDIndD22toD181"                            
## [230] "COVIDIndD22toD91"                             
## [231] "COVIDIndD22toend"                             
## [232] "COVIDIndD36toD181"                            
## [233] "COVIDIndD92toD181"                            
## [234] "COVIDtimeD22toD181"                           
## [235] "COVIDtimeD22toD91"                            
## [236] "COVIDtimeD36toD181"                           
## [237] "COVIDtimeD92toD181"                           
## [238] "COVRDPCT_SWAB1"                               
## [239] "COVRDPCT_SWAB2"                               
## [240] "CTSTAT_SWAB1"                                 
## [241] "CTSTAT_SWAB2"                                 
## [242] "CTVALUE_SWAB1"                                
## [243] "CTVALUE_SWAB2"                                
## [244] "D1_D15_flag"                                  
## [245] "D1_D29_flag"                                  
## [246] "DATE_COLLECT_SWAB1"                           
## [247] "DATE_COLLECT_SWAB2"                           
## [248] "Day147pseudoneutid50_BA.1"                    
## [249] "Day147pseudoneutid50_BA.4.BA.5"               
## [250] "Day147pseudoneutid50_Beta"                    
## [251] "Day147pseudoneutid50_D614G"                   
## [252] "Day147pseudoneutid50_Delta"                   
## [253] "Day15cd4_154_BA.4.5.S1"                       
## [254] "Day15cd4_154_BA.4.5.S1_resp"                  
## [255] "Day15cd4_154_BA.4.5.S2"                       
## [256] "Day15cd4_154_BA.4.5.S2_resp"                  
## [257] "Day15cd4_154_COV2.CON.S1"                     
## [258] "Day15cd4_154_COV2.CON.S1_resp"                
## [259] "Day15cd4_154_COV2.CON.S2"                     
## [260] "Day15cd4_154_COV2.CON.S2_resp"                
## [261] "Day15cd4_154_Wuhan.N"                         
## [262] "Day15cd4_154_Wuhan.N_resp"                    
## [263] "Day15cd4_CXCR5.154_BA.4.5.S1"                 
## [264] "Day15cd4_CXCR5.154_BA.4.5.S1_resp"            
## [265] "Day15cd4_CXCR5.154_BA.4.5.S2"                 
## [266] "Day15cd4_CXCR5.154_BA.4.5.S2_resp"            
## [267] "Day15cd4_CXCR5.154_COV2.CON.S1"               
## [268] "Day15cd4_CXCR5.154_COV2.CON.S1_resp"          
## [269] "Day15cd4_CXCR5.154_COV2.CON.S2"               
## [270] "Day15cd4_CXCR5.154_COV2.CON.S2_resp"          
## [271] "Day15cd4_CXCR5.154_Wuhan.N"                   
## [272] "Day15cd4_CXCR5.154_Wuhan.N_resp"              
## [273] "Day15cd4_CXCR5.IL21_BA.4.5.S1"                
## [274] "Day15cd4_CXCR5.IL21_BA.4.5.S1_resp"           
## [275] "Day15cd4_CXCR5.IL21_BA.4.5.S2"                
## [276] "Day15cd4_CXCR5.IL21_BA.4.5.S2_resp"           
## [277] "Day15cd4_CXCR5.IL21_COV2.CON.S1"              
## [278] "Day15cd4_CXCR5.IL21_COV2.CON.S1_resp"         
## [279] "Day15cd4_CXCR5.IL21_COV2.CON.S2"              
## [280] "Day15cd4_CXCR5.IL21_COV2.CON.S2_resp"         
## [281] "Day15cd4_CXCR5.IL21_Wuhan.N"                  
## [282] "Day15cd4_CXCR5.IL21_Wuhan.N_resp"             
## [283] "Day15cd4_IFNg_BA.4.5.S1"                      
## [284] "Day15cd4_IFNg_BA.4.5.S1_resp"                 
## [285] "Day15cd4_IFNg_BA.4.5.S2"                      
## [286] "Day15cd4_IFNg_BA.4.5.S2_resp"                 
## [287] "Day15cd4_IFNg_COV2.CON.S1"                    
## [288] "Day15cd4_IFNg_COV2.CON.S1_resp"               
## [289] "Day15cd4_IFNg_COV2.CON.S2"                    
## [290] "Day15cd4_IFNg_COV2.CON.S2_resp"               
## [291] "Day15cd4_IFNg_Wuhan.N"                        
## [292] "Day15cd4_IFNg_Wuhan.N_resp"                   
## [293] "Day15cd4_IFNg.IL2_BA.4.5.S1"                  
## [294] "Day15cd4_IFNg.IL2_BA.4.5.S1_resp"             
## [295] "Day15cd4_IFNg.IL2_BA.4.5.S2"                  
## [296] "Day15cd4_IFNg.IL2_BA.4.5.S2_resp"             
## [297] "Day15cd4_IFNg.IL2_COV2.CON.S1"                
## [298] "Day15cd4_IFNg.IL2_COV2.CON.S1_resp"           
## [299] "Day15cd4_IFNg.IL2_COV2.CON.S2"                
## [300] "Day15cd4_IFNg.IL2_COV2.CON.S2_resp"           
## [301] "Day15cd4_IFNg.IL2_Wuhan.N"                    
## [302] "Day15cd4_IFNg.IL2_Wuhan.N_resp"               
## [303] "Day15cd4_IFNg.IL2.154_BA.4.5.S1"              
## [304] "Day15cd4_IFNg.IL2.154_BA.4.5.S1_resp"         
## [305] "Day15cd4_IFNg.IL2.154_BA.4.5.S2"              
## [306] "Day15cd4_IFNg.IL2.154_BA.4.5.S2_resp"         
## [307] "Day15cd4_IFNg.IL2.154_COV2.CON.S1"            
## [308] "Day15cd4_IFNg.IL2.154_COV2.CON.S1_resp"       
## [309] "Day15cd4_IFNg.IL2.154_COV2.CON.S2"            
## [310] "Day15cd4_IFNg.IL2.154_COV2.CON.S2_resp"       
## [311] "Day15cd4_IFNg.IL2.154_Wuhan.N"                
## [312] "Day15cd4_IFNg.IL2.154_Wuhan.N_resp"           
## [313] "Day15cd4_IL17a_BA.4.5.S1"                     
## [314] "Day15cd4_IL17a_BA.4.5.S1_resp"                
## [315] "Day15cd4_IL17a_BA.4.5.S2"                     
## [316] "Day15cd4_IL17a_BA.4.5.S2_resp"                
## [317] "Day15cd4_IL17a_COV2.CON.S1"                   
## [318] "Day15cd4_IL17a_COV2.CON.S1_resp"              
## [319] "Day15cd4_IL17a_COV2.CON.S2"                   
## [320] "Day15cd4_IL17a_COV2.CON.S2_resp"              
## [321] "Day15cd4_IL17a_Wuhan.N"                       
## [322] "Day15cd4_IL17a_Wuhan.N_resp"                  
## [323] "Day15cd4_IL2_BA.4.5.S1"                       
## [324] "Day15cd4_IL2_BA.4.5.S1_resp"                  
## [325] "Day15cd4_IL2_BA.4.5.S2"                       
## [326] "Day15cd4_IL2_BA.4.5.S2_resp"                  
## [327] "Day15cd4_IL2_COV2.CON.S1"                     
## [328] "Day15cd4_IL2_COV2.CON.S1_resp"                
## [329] "Day15cd4_IL2_COV2.CON.S2"                     
## [330] "Day15cd4_IL2_COV2.CON.S2_resp"                
## [331] "Day15cd4_IL2_Wuhan.N"                         
## [332] "Day15cd4_IL2_Wuhan.N_resp"                    
## [333] "Day15cd4_IL21_BA.4.5.S1"                      
## [334] "Day15cd4_IL21_BA.4.5.S1_resp"                 
## [335] "Day15cd4_IL21_BA.4.5.S2"                      
## [336] "Day15cd4_IL21_BA.4.5.S2_resp"                 
## [337] "Day15cd4_IL21_COV2.CON.S1"                    
## [338] "Day15cd4_IL21_COV2.CON.S1_resp"               
## [339] "Day15cd4_IL21_COV2.CON.S2"                    
## [340] "Day15cd4_IL21_COV2.CON.S2_resp"               
## [341] "Day15cd4_IL21_Wuhan.N"                        
## [342] "Day15cd4_IL21_Wuhan.N_resp"                   
## [343] "Day15cd4_IL4.154_BA.4.5.S1"                   
## [344] "Day15cd4_IL4.154_BA.4.5.S1_resp"              
## [345] "Day15cd4_IL4.154_BA.4.5.S2"                   
## [346] "Day15cd4_IL4.154_BA.4.5.S2_resp"              
## [347] "Day15cd4_IL4.154_COV2.CON.S1"                 
## [348] "Day15cd4_IL4.154_COV2.CON.S1_resp"            
## [349] "Day15cd4_IL4.154_COV2.CON.S2"                 
## [350] "Day15cd4_IL4.154_COV2.CON.S2_resp"            
## [351] "Day15cd4_IL4.154_Wuhan.N"                     
## [352] "Day15cd4_IL4.154_Wuhan.N_resp"                
## [353] "Day15cd4_IL4.IL5.IL13.154_BA.4.5.S1"          
## [354] "Day15cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp"     
## [355] "Day15cd4_IL4.IL5.IL13.154_BA.4.5.S2"          
## [356] "Day15cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp"     
## [357] "Day15cd4_IL4.IL5.IL13.154_COV2.CON.S1"        
## [358] "Day15cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp"   
## [359] "Day15cd4_IL4.IL5.IL13.154_COV2.CON.S2"        
## [360] "Day15cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp"   
## [361] "Day15cd4_IL4.IL5.IL13.154_Wuhan.N"            
## [362] "Day15cd4_IL4.IL5.IL13.154_Wuhan.N_resp"       
## [363] "Day15cd4_IL5.IL13.154_BA.4.5.S1"              
## [364] "Day15cd4_IL5.IL13.154_BA.4.5.S1_resp"         
## [365] "Day15cd4_IL5.IL13.154_BA.4.5.S2"              
## [366] "Day15cd4_IL5.IL13.154_BA.4.5.S2_resp"         
## [367] "Day15cd4_IL5.IL13.154_COV2.CON.S1"            
## [368] "Day15cd4_IL5.IL13.154_COV2.CON.S1_resp"       
## [369] "Day15cd4_IL5.IL13.154_COV2.CON.S2"            
## [370] "Day15cd4_IL5.IL13.154_COV2.CON.S2_resp"       
## [371] "Day15cd4_IL5.IL13.154_Wuhan.N"                
## [372] "Day15cd4_IL5.IL13.154_Wuhan.N_resp"           
## [373] "Day15cd4_TNFa_BA.4.5.S1"                      
## [374] "Day15cd4_TNFa_BA.4.5.S1_resp"                 
## [375] "Day15cd4_TNFa_BA.4.5.S2"                      
## [376] "Day15cd4_TNFa_BA.4.5.S2_resp"                 
## [377] "Day15cd4_TNFa_COV2.CON.S1"                    
## [378] "Day15cd4_TNFa_COV2.CON.S1_resp"               
## [379] "Day15cd4_TNFa_COV2.CON.S2"                    
## [380] "Day15cd4_TNFa_COV2.CON.S2_resp"               
## [381] "Day15cd4_TNFa_Wuhan.N"                        
## [382] "Day15cd4_TNFa_Wuhan.N_resp"                   
## [383] "Day15cd8_IFNg_BA.4.5.S1"                      
## [384] "Day15cd8_IFNg_BA.4.5.S1_resp"                 
## [385] "Day15cd8_IFNg_BA.4.5.S2"                      
## [386] "Day15cd8_IFNg_BA.4.5.S2_resp"                 
## [387] "Day15cd8_IFNg_COV2.CON.S1"                    
## [388] "Day15cd8_IFNg_COV2.CON.S1_resp"               
## [389] "Day15cd8_IFNg_COV2.CON.S2"                    
## [390] "Day15cd8_IFNg_COV2.CON.S2_resp"               
## [391] "Day15cd8_IFNg_Wuhan.N"                        
## [392] "Day15cd8_IFNg_Wuhan.N_resp"                   
## [393] "Day15cd8_IFNg.IL2_BA.4.5.S1"                  
## [394] "Day15cd8_IFNg.IL2_BA.4.5.S1_resp"             
## [395] "Day15cd8_IFNg.IL2_BA.4.5.S2"                  
## [396] "Day15cd8_IFNg.IL2_BA.4.5.S2_resp"             
## [397] "Day15cd8_IFNg.IL2_COV2.CON.S1"                
## [398] "Day15cd8_IFNg.IL2_COV2.CON.S1_resp"           
## [399] "Day15cd8_IFNg.IL2_COV2.CON.S2"                
## [400] "Day15cd8_IFNg.IL2_COV2.CON.S2_resp"           
## [401] "Day15cd8_IFNg.IL2_Wuhan.N"                    
## [402] "Day15cd8_IFNg.IL2_Wuhan.N_resp"               
## [403] "Day15cd8_IFNg.IL2.TNFa_BA.4.5.S1"             
## [404] "Day15cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp"        
## [405] "Day15cd8_IFNg.IL2.TNFa_BA.4.5.S2"             
## [406] "Day15cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp"        
## [407] "Day15cd8_IFNg.IL2.TNFa_COV2.CON.S1"           
## [408] "Day15cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp"      
## [409] "Day15cd8_IFNg.IL2.TNFa_COV2.CON.S2"           
## [410] "Day15cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp"      
## [411] "Day15cd8_IFNg.IL2.TNFa_Wuhan.N"               
## [412] "Day15cd8_IFNg.IL2.TNFa_Wuhan.N_resp"          
## [413] "Day15cd8_IL2_BA.4.5.S1"                       
## [414] "Day15cd8_IL2_BA.4.5.S1_resp"                  
## [415] "Day15cd8_IL2_BA.4.5.S2"                       
## [416] "Day15cd8_IL2_BA.4.5.S2_resp"                  
## [417] "Day15cd8_IL2_COV2.CON.S1"                     
## [418] "Day15cd8_IL2_COV2.CON.S1_resp"                
## [419] "Day15cd8_IL2_COV2.CON.S2"                     
## [420] "Day15cd8_IL2_COV2.CON.S2_resp"                
## [421] "Day15cd8_IL2_Wuhan.N"                         
## [422] "Day15cd8_IL2_Wuhan.N_resp"                    
## [423] "Day15cd8_TNFa_BA.4.5.S1"                      
## [424] "Day15cd8_TNFa_BA.4.5.S1_resp"                 
## [425] "Day15cd8_TNFa_BA.4.5.S2"                      
## [426] "Day15cd8_TNFa_BA.4.5.S2_resp"                 
## [427] "Day15cd8_TNFa_COV2.CON.S1"                    
## [428] "Day15cd8_TNFa_COV2.CON.S1_resp"               
## [429] "Day15cd8_TNFa_COV2.CON.S2"                    
## [430] "Day15cd8_TNFa_COV2.CON.S2_resp"               
## [431] "Day15cd8_TNFa_Wuhan.N"                        
## [432] "Day15cd8_TNFa_Wuhan.N_resp"                   
## [433] "Day15pseudoneutid50_BA.1"                     
## [434] "Day15pseudoneutid50_BA.4.BA.5"                
## [435] "Day15pseudoneutid50_Beta"                     
## [436] "Day15pseudoneutid50_D614G"                    
## [437] "Day15pseudoneutid50_Delta"                    
## [438] "Day15pseudoneutid50Duke_BA.2.12.1"            
## [439] "Day181cd4_154_BA.4.5.S1"                      
## [440] "Day181cd4_154_BA.4.5.S1_resp"                 
## [441] "Day181cd4_154_BA.4.5.S2"                      
## [442] "Day181cd4_154_BA.4.5.S2_resp"                 
## [443] "Day181cd4_154_COV2.CON.S1"                    
## [444] "Day181cd4_154_COV2.CON.S1_resp"               
## [445] "Day181cd4_154_COV2.CON.S2"                    
## [446] "Day181cd4_154_COV2.CON.S2_resp"               
## [447] "Day181cd4_154_Wuhan.N"                        
## [448] "Day181cd4_154_Wuhan.N_resp"                   
## [449] "Day181cd4_CXCR5.154_BA.4.5.S1"                
## [450] "Day181cd4_CXCR5.154_BA.4.5.S1_resp"           
## [451] "Day181cd4_CXCR5.154_BA.4.5.S2"                
## [452] "Day181cd4_CXCR5.154_BA.4.5.S2_resp"           
## [453] "Day181cd4_CXCR5.154_COV2.CON.S1"              
## [454] "Day181cd4_CXCR5.154_COV2.CON.S1_resp"         
## [455] "Day181cd4_CXCR5.154_COV2.CON.S2"              
## [456] "Day181cd4_CXCR5.154_COV2.CON.S2_resp"         
## [457] "Day181cd4_CXCR5.154_Wuhan.N"                  
## [458] "Day181cd4_CXCR5.154_Wuhan.N_resp"             
## [459] "Day181cd4_CXCR5.IL21_BA.4.5.S1"               
## [460] "Day181cd4_CXCR5.IL21_BA.4.5.S1_resp"          
## [461] "Day181cd4_CXCR5.IL21_BA.4.5.S2"               
## [462] "Day181cd4_CXCR5.IL21_BA.4.5.S2_resp"          
## [463] "Day181cd4_CXCR5.IL21_COV2.CON.S1"             
## [464] "Day181cd4_CXCR5.IL21_COV2.CON.S1_resp"        
## [465] "Day181cd4_CXCR5.IL21_COV2.CON.S2"             
## [466] "Day181cd4_CXCR5.IL21_COV2.CON.S2_resp"        
## [467] "Day181cd4_CXCR5.IL21_Wuhan.N"                 
## [468] "Day181cd4_CXCR5.IL21_Wuhan.N_resp"            
## [469] "Day181cd4_IFNg_BA.4.5.S1"                     
## [470] "Day181cd4_IFNg_BA.4.5.S1_resp"                
## [471] "Day181cd4_IFNg_BA.4.5.S2"                     
## [472] "Day181cd4_IFNg_BA.4.5.S2_resp"                
## [473] "Day181cd4_IFNg_COV2.CON.S1"                   
## [474] "Day181cd4_IFNg_COV2.CON.S1_resp"              
## [475] "Day181cd4_IFNg_COV2.CON.S2"                   
## [476] "Day181cd4_IFNg_COV2.CON.S2_resp"              
## [477] "Day181cd4_IFNg_Wuhan.N"                       
## [478] "Day181cd4_IFNg_Wuhan.N_resp"                  
## [479] "Day181cd4_IFNg.IL2_BA.4.5.S1"                 
## [480] "Day181cd4_IFNg.IL2_BA.4.5.S1_resp"            
## [481] "Day181cd4_IFNg.IL2_BA.4.5.S2"                 
## [482] "Day181cd4_IFNg.IL2_BA.4.5.S2_resp"            
## [483] "Day181cd4_IFNg.IL2_COV2.CON.S1"               
## [484] "Day181cd4_IFNg.IL2_COV2.CON.S1_resp"          
## [485] "Day181cd4_IFNg.IL2_COV2.CON.S2"               
## [486] "Day181cd4_IFNg.IL2_COV2.CON.S2_resp"          
## [487] "Day181cd4_IFNg.IL2_Wuhan.N"                   
## [488] "Day181cd4_IFNg.IL2_Wuhan.N_resp"              
## [489] "Day181cd4_IFNg.IL2.154_BA.4.5.S1"             
## [490] "Day181cd4_IFNg.IL2.154_BA.4.5.S1_resp"        
## [491] "Day181cd4_IFNg.IL2.154_BA.4.5.S2"             
## [492] "Day181cd4_IFNg.IL2.154_BA.4.5.S2_resp"        
## [493] "Day181cd4_IFNg.IL2.154_COV2.CON.S1"           
## [494] "Day181cd4_IFNg.IL2.154_COV2.CON.S1_resp"      
## [495] "Day181cd4_IFNg.IL2.154_COV2.CON.S2"           
## [496] "Day181cd4_IFNg.IL2.154_COV2.CON.S2_resp"      
## [497] "Day181cd4_IFNg.IL2.154_Wuhan.N"               
## [498] "Day181cd4_IFNg.IL2.154_Wuhan.N_resp"          
## [499] "Day181cd4_IL17a_BA.4.5.S1"                    
## [500] "Day181cd4_IL17a_BA.4.5.S1_resp"               
## [501] "Day181cd4_IL17a_BA.4.5.S2"                    
## [502] "Day181cd4_IL17a_BA.4.5.S2_resp"               
## [503] "Day181cd4_IL17a_COV2.CON.S1"                  
## [504] "Day181cd4_IL17a_COV2.CON.S1_resp"             
## [505] "Day181cd4_IL17a_COV2.CON.S2"                  
## [506] "Day181cd4_IL17a_COV2.CON.S2_resp"             
## [507] "Day181cd4_IL17a_Wuhan.N"                      
## [508] "Day181cd4_IL17a_Wuhan.N_resp"                 
## [509] "Day181cd4_IL2_BA.4.5.S1"                      
## [510] "Day181cd4_IL2_BA.4.5.S1_resp"                 
## [511] "Day181cd4_IL2_BA.4.5.S2"                      
## [512] "Day181cd4_IL2_BA.4.5.S2_resp"                 
## [513] "Day181cd4_IL2_COV2.CON.S1"                    
## [514] "Day181cd4_IL2_COV2.CON.S1_resp"               
## [515] "Day181cd4_IL2_COV2.CON.S2"                    
## [516] "Day181cd4_IL2_COV2.CON.S2_resp"               
## [517] "Day181cd4_IL2_Wuhan.N"                        
## [518] "Day181cd4_IL2_Wuhan.N_resp"                   
## [519] "Day181cd4_IL21_BA.4.5.S1"                     
## [520] "Day181cd4_IL21_BA.4.5.S1_resp"                
## [521] "Day181cd4_IL21_BA.4.5.S2"                     
## [522] "Day181cd4_IL21_BA.4.5.S2_resp"                
## [523] "Day181cd4_IL21_COV2.CON.S1"                   
## [524] "Day181cd4_IL21_COV2.CON.S1_resp"              
## [525] "Day181cd4_IL21_COV2.CON.S2"                   
## [526] "Day181cd4_IL21_COV2.CON.S2_resp"              
## [527] "Day181cd4_IL21_Wuhan.N"                       
## [528] "Day181cd4_IL21_Wuhan.N_resp"                  
## [529] "Day181cd4_IL4.154_BA.4.5.S1"                  
## [530] "Day181cd4_IL4.154_BA.4.5.S1_resp"             
## [531] "Day181cd4_IL4.154_BA.4.5.S2"                  
## [532] "Day181cd4_IL4.154_BA.4.5.S2_resp"             
## [533] "Day181cd4_IL4.154_COV2.CON.S1"                
## [534] "Day181cd4_IL4.154_COV2.CON.S1_resp"           
## [535] "Day181cd4_IL4.154_COV2.CON.S2"                
## [536] "Day181cd4_IL4.154_COV2.CON.S2_resp"           
## [537] "Day181cd4_IL4.154_Wuhan.N"                    
## [538] "Day181cd4_IL4.154_Wuhan.N_resp"               
## [539] "Day181cd4_IL4.IL5.IL13.154_BA.4.5.S1"         
## [540] "Day181cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp"    
## [541] "Day181cd4_IL4.IL5.IL13.154_BA.4.5.S2"         
## [542] "Day181cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp"    
## [543] "Day181cd4_IL4.IL5.IL13.154_COV2.CON.S1"       
## [544] "Day181cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp"  
## [545] "Day181cd4_IL4.IL5.IL13.154_COV2.CON.S2"       
## [546] "Day181cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp"  
## [547] "Day181cd4_IL4.IL5.IL13.154_Wuhan.N"           
## [548] "Day181cd4_IL4.IL5.IL13.154_Wuhan.N_resp"      
## [549] "Day181cd4_IL5.IL13.154_BA.4.5.S1"             
## [550] "Day181cd4_IL5.IL13.154_BA.4.5.S1_resp"        
## [551] "Day181cd4_IL5.IL13.154_BA.4.5.S2"             
## [552] "Day181cd4_IL5.IL13.154_BA.4.5.S2_resp"        
## [553] "Day181cd4_IL5.IL13.154_COV2.CON.S1"           
## [554] "Day181cd4_IL5.IL13.154_COV2.CON.S1_resp"      
## [555] "Day181cd4_IL5.IL13.154_COV2.CON.S2"           
## [556] "Day181cd4_IL5.IL13.154_COV2.CON.S2_resp"      
## [557] "Day181cd4_IL5.IL13.154_Wuhan.N"               
## [558] "Day181cd4_IL5.IL13.154_Wuhan.N_resp"          
## [559] "Day181cd4_TNFa_BA.4.5.S1"                     
## [560] "Day181cd4_TNFa_BA.4.5.S1_resp"                
## [561] "Day181cd4_TNFa_BA.4.5.S2"                     
## [562] "Day181cd4_TNFa_BA.4.5.S2_resp"                
## [563] "Day181cd4_TNFa_COV2.CON.S1"                   
## [564] "Day181cd4_TNFa_COV2.CON.S1_resp"              
## [565] "Day181cd4_TNFa_COV2.CON.S2"                   
## [566] "Day181cd4_TNFa_COV2.CON.S2_resp"              
## [567] "Day181cd4_TNFa_Wuhan.N"                       
## [568] "Day181cd4_TNFa_Wuhan.N_resp"                  
## [569] "Day181cd8_IFNg_BA.4.5.S1"                     
## [570] "Day181cd8_IFNg_BA.4.5.S1_resp"                
## [571] "Day181cd8_IFNg_BA.4.5.S2"                     
## [572] "Day181cd8_IFNg_BA.4.5.S2_resp"                
## [573] "Day181cd8_IFNg_COV2.CON.S1"                   
## [574] "Day181cd8_IFNg_COV2.CON.S1_resp"              
## [575] "Day181cd8_IFNg_COV2.CON.S2"                   
## [576] "Day181cd8_IFNg_COV2.CON.S2_resp"              
## [577] "Day181cd8_IFNg_Wuhan.N"                       
## [578] "Day181cd8_IFNg_Wuhan.N_resp"                  
## [579] "Day181cd8_IFNg.IL2_BA.4.5.S1"                 
## [580] "Day181cd8_IFNg.IL2_BA.4.5.S1_resp"            
## [581] "Day181cd8_IFNg.IL2_BA.4.5.S2"                 
## [582] "Day181cd8_IFNg.IL2_BA.4.5.S2_resp"            
## [583] "Day181cd8_IFNg.IL2_COV2.CON.S1"               
## [584] "Day181cd8_IFNg.IL2_COV2.CON.S1_resp"          
## [585] "Day181cd8_IFNg.IL2_COV2.CON.S2"               
## [586] "Day181cd8_IFNg.IL2_COV2.CON.S2_resp"          
## [587] "Day181cd8_IFNg.IL2_Wuhan.N"                   
## [588] "Day181cd8_IFNg.IL2_Wuhan.N_resp"              
## [589] "Day181cd8_IFNg.IL2.TNFa_BA.4.5.S1"            
## [590] "Day181cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp"       
## [591] "Day181cd8_IFNg.IL2.TNFa_BA.4.5.S2"            
## [592] "Day181cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp"       
## [593] "Day181cd8_IFNg.IL2.TNFa_COV2.CON.S1"          
## [594] "Day181cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp"     
## [595] "Day181cd8_IFNg.IL2.TNFa_COV2.CON.S2"          
## [596] "Day181cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp"     
## [597] "Day181cd8_IFNg.IL2.TNFa_Wuhan.N"              
## [598] "Day181cd8_IFNg.IL2.TNFa_Wuhan.N_resp"         
## [599] "Day181cd8_IL2_BA.4.5.S1"                      
## [600] "Day181cd8_IL2_BA.4.5.S1_resp"                 
## [601] "Day181cd8_IL2_BA.4.5.S2"                      
## [602] "Day181cd8_IL2_BA.4.5.S2_resp"                 
## [603] "Day181cd8_IL2_COV2.CON.S1"                    
## [604] "Day181cd8_IL2_COV2.CON.S1_resp"               
## [605] "Day181cd8_IL2_COV2.CON.S2"                    
## [606] "Day181cd8_IL2_COV2.CON.S2_resp"               
## [607] "Day181cd8_IL2_Wuhan.N"                        
## [608] "Day181cd8_IL2_Wuhan.N_resp"                   
## [609] "Day181cd8_TNFa_BA.4.5.S1"                     
## [610] "Day181cd8_TNFa_BA.4.5.S1_resp"                
## [611] "Day181cd8_TNFa_BA.4.5.S2"                     
## [612] "Day181cd8_TNFa_BA.4.5.S2_resp"                
## [613] "Day181cd8_TNFa_COV2.CON.S1"                   
## [614] "Day181cd8_TNFa_COV2.CON.S1_resp"              
## [615] "Day181cd8_TNFa_COV2.CON.S2"                   
## [616] "Day181cd8_TNFa_COV2.CON.S2_resp"              
## [617] "Day181cd8_TNFa_Wuhan.N"                       
## [618] "Day181cd8_TNFa_Wuhan.N_resp"                  
## [619] "Day181pseudoneutid50_BA.1"                    
## [620] "Day181pseudoneutid50_BA.4.BA.5"               
## [621] "Day181pseudoneutid50_Beta"                    
## [622] "Day181pseudoneutid50_D614G"                   
## [623] "Day181pseudoneutid50_Delta"                   
## [624] "Day29pseudoneutid50_BA.1"                     
## [625] "Day29pseudoneutid50_BA.4.BA.5"                
## [626] "Day29pseudoneutid50_Beta"                     
## [627] "Day29pseudoneutid50_D614G"                    
## [628] "Day29pseudoneutid50_Delta"                    
## [629] "Day85pseudoneutid50_BA.1"                     
## [630] "Day85pseudoneutid50_BA.4.BA.5"                
## [631] "Day85pseudoneutid50_Beta"                     
## [632] "Day85pseudoneutid50_D614G"                    
## [633] "Day85pseudoneutid50_Delta"                    
## [634] "Day91cd4_154_BA.4.5.S1"                       
## [635] "Day91cd4_154_BA.4.5.S1_resp"                  
## [636] "Day91cd4_154_BA.4.5.S2"                       
## [637] "Day91cd4_154_BA.4.5.S2_resp"                  
## [638] "Day91cd4_154_COV2.CON.S1"                     
## [639] "Day91cd4_154_COV2.CON.S1_resp"                
## [640] "Day91cd4_154_COV2.CON.S2"                     
## [641] "Day91cd4_154_COV2.CON.S2_resp"                
## [642] "Day91cd4_154_Wuhan.N"                         
## [643] "Day91cd4_154_Wuhan.N_resp"                    
## [644] "Day91cd4_CXCR5.154_BA.4.5.S1"                 
## [645] "Day91cd4_CXCR5.154_BA.4.5.S1_resp"            
## [646] "Day91cd4_CXCR5.154_BA.4.5.S2"                 
## [647] "Day91cd4_CXCR5.154_BA.4.5.S2_resp"            
## [648] "Day91cd4_CXCR5.154_COV2.CON.S1"               
## [649] "Day91cd4_CXCR5.154_COV2.CON.S1_resp"          
## [650] "Day91cd4_CXCR5.154_COV2.CON.S2"               
## [651] "Day91cd4_CXCR5.154_COV2.CON.S2_resp"          
## [652] "Day91cd4_CXCR5.154_Wuhan.N"                   
## [653] "Day91cd4_CXCR5.154_Wuhan.N_resp"              
## [654] "Day91cd4_CXCR5.IL21_BA.4.5.S1"                
## [655] "Day91cd4_CXCR5.IL21_BA.4.5.S1_resp"           
## [656] "Day91cd4_CXCR5.IL21_BA.4.5.S2"                
## [657] "Day91cd4_CXCR5.IL21_BA.4.5.S2_resp"           
## [658] "Day91cd4_CXCR5.IL21_COV2.CON.S1"              
## [659] "Day91cd4_CXCR5.IL21_COV2.CON.S1_resp"         
## [660] "Day91cd4_CXCR5.IL21_COV2.CON.S2"              
## [661] "Day91cd4_CXCR5.IL21_COV2.CON.S2_resp"         
## [662] "Day91cd4_CXCR5.IL21_Wuhan.N"                  
## [663] "Day91cd4_CXCR5.IL21_Wuhan.N_resp"             
## [664] "Day91cd4_IFNg_BA.4.5.S1"                      
## [665] "Day91cd4_IFNg_BA.4.5.S1_resp"                 
## [666] "Day91cd4_IFNg_BA.4.5.S2"                      
## [667] "Day91cd4_IFNg_BA.4.5.S2_resp"                 
## [668] "Day91cd4_IFNg_COV2.CON.S1"                    
## [669] "Day91cd4_IFNg_COV2.CON.S1_resp"               
## [670] "Day91cd4_IFNg_COV2.CON.S2"                    
## [671] "Day91cd4_IFNg_COV2.CON.S2_resp"               
## [672] "Day91cd4_IFNg_Wuhan.N"                        
## [673] "Day91cd4_IFNg_Wuhan.N_resp"                   
## [674] "Day91cd4_IFNg.IL2_BA.4.5.S1"                  
## [675] "Day91cd4_IFNg.IL2_BA.4.5.S1_resp"             
## [676] "Day91cd4_IFNg.IL2_BA.4.5.S2"                  
## [677] "Day91cd4_IFNg.IL2_BA.4.5.S2_resp"             
## [678] "Day91cd4_IFNg.IL2_COV2.CON.S1"                
## [679] "Day91cd4_IFNg.IL2_COV2.CON.S1_resp"           
## [680] "Day91cd4_IFNg.IL2_COV2.CON.S2"                
## [681] "Day91cd4_IFNg.IL2_COV2.CON.S2_resp"           
## [682] "Day91cd4_IFNg.IL2_Wuhan.N"                    
## [683] "Day91cd4_IFNg.IL2_Wuhan.N_resp"               
## [684] "Day91cd4_IFNg.IL2.154_BA.4.5.S1"              
## [685] "Day91cd4_IFNg.IL2.154_BA.4.5.S1_resp"         
## [686] "Day91cd4_IFNg.IL2.154_BA.4.5.S2"              
## [687] "Day91cd4_IFNg.IL2.154_BA.4.5.S2_resp"         
## [688] "Day91cd4_IFNg.IL2.154_COV2.CON.S1"            
## [689] "Day91cd4_IFNg.IL2.154_COV2.CON.S1_resp"       
## [690] "Day91cd4_IFNg.IL2.154_COV2.CON.S2"            
## [691] "Day91cd4_IFNg.IL2.154_COV2.CON.S2_resp"       
## [692] "Day91cd4_IFNg.IL2.154_Wuhan.N"                
## [693] "Day91cd4_IFNg.IL2.154_Wuhan.N_resp"           
## [694] "Day91cd4_IL17a_BA.4.5.S1"                     
## [695] "Day91cd4_IL17a_BA.4.5.S1_resp"                
## [696] "Day91cd4_IL17a_BA.4.5.S2"                     
## [697] "Day91cd4_IL17a_BA.4.5.S2_resp"                
## [698] "Day91cd4_IL17a_COV2.CON.S1"                   
## [699] "Day91cd4_IL17a_COV2.CON.S1_resp"              
## [700] "Day91cd4_IL17a_COV2.CON.S2"                   
## [701] "Day91cd4_IL17a_COV2.CON.S2_resp"              
## [702] "Day91cd4_IL17a_Wuhan.N"                       
## [703] "Day91cd4_IL17a_Wuhan.N_resp"                  
## [704] "Day91cd4_IL2_BA.4.5.S1"                       
## [705] "Day91cd4_IL2_BA.4.5.S1_resp"                  
## [706] "Day91cd4_IL2_BA.4.5.S2"                       
## [707] "Day91cd4_IL2_BA.4.5.S2_resp"                  
## [708] "Day91cd4_IL2_COV2.CON.S1"                     
## [709] "Day91cd4_IL2_COV2.CON.S1_resp"                
## [710] "Day91cd4_IL2_COV2.CON.S2"                     
## [711] "Day91cd4_IL2_COV2.CON.S2_resp"                
## [712] "Day91cd4_IL2_Wuhan.N"                         
## [713] "Day91cd4_IL2_Wuhan.N_resp"                    
## [714] "Day91cd4_IL21_BA.4.5.S1"                      
## [715] "Day91cd4_IL21_BA.4.5.S1_resp"                 
## [716] "Day91cd4_IL21_BA.4.5.S2"                      
## [717] "Day91cd4_IL21_BA.4.5.S2_resp"                 
## [718] "Day91cd4_IL21_COV2.CON.S1"                    
## [719] "Day91cd4_IL21_COV2.CON.S1_resp"               
## [720] "Day91cd4_IL21_COV2.CON.S2"                    
## [721] "Day91cd4_IL21_COV2.CON.S2_resp"               
## [722] "Day91cd4_IL21_Wuhan.N"                        
## [723] "Day91cd4_IL21_Wuhan.N_resp"                   
## [724] "Day91cd4_IL4.154_BA.4.5.S1"                   
## [725] "Day91cd4_IL4.154_BA.4.5.S1_resp"              
## [726] "Day91cd4_IL4.154_BA.4.5.S2"                   
## [727] "Day91cd4_IL4.154_BA.4.5.S2_resp"              
## [728] "Day91cd4_IL4.154_COV2.CON.S1"                 
## [729] "Day91cd4_IL4.154_COV2.CON.S1_resp"            
## [730] "Day91cd4_IL4.154_COV2.CON.S2"                 
## [731] "Day91cd4_IL4.154_COV2.CON.S2_resp"            
## [732] "Day91cd4_IL4.154_Wuhan.N"                     
## [733] "Day91cd4_IL4.154_Wuhan.N_resp"                
## [734] "Day91cd4_IL4.IL5.IL13.154_BA.4.5.S1"          
## [735] "Day91cd4_IL4.IL5.IL13.154_BA.4.5.S1_resp"     
## [736] "Day91cd4_IL4.IL5.IL13.154_BA.4.5.S2"          
## [737] "Day91cd4_IL4.IL5.IL13.154_BA.4.5.S2_resp"     
## [738] "Day91cd4_IL4.IL5.IL13.154_COV2.CON.S1"        
## [739] "Day91cd4_IL4.IL5.IL13.154_COV2.CON.S1_resp"   
## [740] "Day91cd4_IL4.IL5.IL13.154_COV2.CON.S2"        
## [741] "Day91cd4_IL4.IL5.IL13.154_COV2.CON.S2_resp"   
## [742] "Day91cd4_IL4.IL5.IL13.154_Wuhan.N"            
## [743] "Day91cd4_IL4.IL5.IL13.154_Wuhan.N_resp"       
## [744] "Day91cd4_IL5.IL13.154_BA.4.5.S1"              
## [745] "Day91cd4_IL5.IL13.154_BA.4.5.S1_resp"         
## [746] "Day91cd4_IL5.IL13.154_BA.4.5.S2"              
## [747] "Day91cd4_IL5.IL13.154_BA.4.5.S2_resp"         
## [748] "Day91cd4_IL5.IL13.154_COV2.CON.S1"            
## [749] "Day91cd4_IL5.IL13.154_COV2.CON.S1_resp"       
## [750] "Day91cd4_IL5.IL13.154_COV2.CON.S2"            
## [751] "Day91cd4_IL5.IL13.154_COV2.CON.S2_resp"       
## [752] "Day91cd4_IL5.IL13.154_Wuhan.N"                
## [753] "Day91cd4_IL5.IL13.154_Wuhan.N_resp"           
## [754] "Day91cd4_TNFa_BA.4.5.S1"                      
## [755] "Day91cd4_TNFa_BA.4.5.S1_resp"                 
## [756] "Day91cd4_TNFa_BA.4.5.S2"                      
## [757] "Day91cd4_TNFa_BA.4.5.S2_resp"                 
## [758] "Day91cd4_TNFa_COV2.CON.S1"                    
## [759] "Day91cd4_TNFa_COV2.CON.S1_resp"               
## [760] "Day91cd4_TNFa_COV2.CON.S2"                    
## [761] "Day91cd4_TNFa_COV2.CON.S2_resp"               
## [762] "Day91cd4_TNFa_Wuhan.N"                        
## [763] "Day91cd4_TNFa_Wuhan.N_resp"                   
## [764] "Day91cd8_IFNg_BA.4.5.S1"                      
## [765] "Day91cd8_IFNg_BA.4.5.S1_resp"                 
## [766] "Day91cd8_IFNg_BA.4.5.S2"                      
## [767] "Day91cd8_IFNg_BA.4.5.S2_resp"                 
## [768] "Day91cd8_IFNg_COV2.CON.S1"                    
## [769] "Day91cd8_IFNg_COV2.CON.S1_resp"               
## [770] "Day91cd8_IFNg_COV2.CON.S2"                    
## [771] "Day91cd8_IFNg_COV2.CON.S2_resp"               
## [772] "Day91cd8_IFNg_Wuhan.N"                        
## [773] "Day91cd8_IFNg_Wuhan.N_resp"                   
## [774] "Day91cd8_IFNg.IL2_BA.4.5.S1"                  
## [775] "Day91cd8_IFNg.IL2_BA.4.5.S1_resp"             
## [776] "Day91cd8_IFNg.IL2_BA.4.5.S2"                  
## [777] "Day91cd8_IFNg.IL2_BA.4.5.S2_resp"             
## [778] "Day91cd8_IFNg.IL2_COV2.CON.S1"                
## [779] "Day91cd8_IFNg.IL2_COV2.CON.S1_resp"           
## [780] "Day91cd8_IFNg.IL2_COV2.CON.S2"                
## [781] "Day91cd8_IFNg.IL2_COV2.CON.S2_resp"           
## [782] "Day91cd8_IFNg.IL2_Wuhan.N"                    
## [783] "Day91cd8_IFNg.IL2_Wuhan.N_resp"               
## [784] "Day91cd8_IFNg.IL2.TNFa_BA.4.5.S1"             
## [785] "Day91cd8_IFNg.IL2.TNFa_BA.4.5.S1_resp"        
## [786] "Day91cd8_IFNg.IL2.TNFa_BA.4.5.S2"             
## [787] "Day91cd8_IFNg.IL2.TNFa_BA.4.5.S2_resp"        
## [788] "Day91cd8_IFNg.IL2.TNFa_COV2.CON.S1"           
## [789] "Day91cd8_IFNg.IL2.TNFa_COV2.CON.S1_resp"      
## [790] "Day91cd8_IFNg.IL2.TNFa_COV2.CON.S2"           
## [791] "Day91cd8_IFNg.IL2.TNFa_COV2.CON.S2_resp"      
## [792] "Day91cd8_IFNg.IL2.TNFa_Wuhan.N"               
## [793] "Day91cd8_IFNg.IL2.TNFa_Wuhan.N_resp"          
## [794] "Day91cd8_IL2_BA.4.5.S1"                       
## [795] "Day91cd8_IL2_BA.4.5.S1_resp"                  
## [796] "Day91cd8_IL2_BA.4.5.S2"                       
## [797] "Day91cd8_IL2_BA.4.5.S2_resp"                  
## [798] "Day91cd8_IL2_COV2.CON.S1"                     
## [799] "Day91cd8_IL2_COV2.CON.S1_resp"                
## [800] "Day91cd8_IL2_COV2.CON.S2"                     
## [801] "Day91cd8_IL2_COV2.CON.S2_resp"                
## [802] "Day91cd8_IL2_Wuhan.N"                         
## [803] "Day91cd8_IL2_Wuhan.N_resp"                    
## [804] "Day91cd8_TNFa_BA.4.5.S1"                      
## [805] "Day91cd8_TNFa_BA.4.5.S1_resp"                 
## [806] "Day91cd8_TNFa_BA.4.5.S2"                      
## [807] "Day91cd8_TNFa_BA.4.5.S2_resp"                 
## [808] "Day91cd8_TNFa_COV2.CON.S1"                    
## [809] "Day91cd8_TNFa_COV2.CON.S1_resp"               
## [810] "Day91cd8_TNFa_COV2.CON.S2"                    
## [811] "Day91cd8_TNFa_COV2.CON.S2_resp"               
## [812] "Day91cd8_TNFa_Wuhan.N"                        
## [813] "Day91cd8_TNFa_Wuhan.N_resp"                   
## [814] "Day91pseudoneutid50_BA.1"                     
## [815] "Day91pseudoneutid50_BA.4.BA.5"                
## [816] "Day91pseudoneutid50_Beta"                     
## [817] "Day91pseudoneutid50_D614G"                    
## [818] "Day91pseudoneutid50_Delta"                    
## [819] "early_term"                                   
## [820] "early_term_date"                              
## [821] "early_term_date_imp"                          
## [822] "EarlyendpointD15"                             
## [823] "eligibility_deviation"                        
## [824] "EthnicityHispanic"                            
## [825] "EthnicityNotreported"                         
## [826] "first_Npos_date"                              
## [827] "HSTRDPCT_SWAB1"                               
## [828] "HSTRDPCT_SWAB2"                               
## [829] "ics"                                          
## [830] "Immunemarkerset"                              
## [831] "ImmunemarkersetD92toD181"                     
## [832] "infect_date1"                                 
## [833] "infect_date2"                                 
## [834] "last_contact_date"                            
## [835] "Multiracial"                                  
## [836] "N_status_1.0"                                 
## [837] "N_status_15.2"                                
## [838] "N_status_181.14"                              
## [839] "N_status_271.14"                              
## [840] "N_status_29.2"                                
## [841] "N_status_91.7"                                
## [842] "naive"                                        
## [843] "NAntibody"                                    
## [844] "NatAmer"                                      
## [845] "NumberdaysD15toD181"                          
## [846] "NumberdaysD15toD29"                           
## [847] "NumberdaysD15toD91"                           
## [848] "oos_boost"                                    
## [849] "oos_boost_date"                               
## [850] "oos_boost_date_imp"                           
## [851] "PacIsl"                                       
## [852] "PANGOLIN_SWAB1"                               
## [853] "PANGOLIN_SWAB2"                               
## [854] "PANGOVER_SWAB1"                               
## [855] "PANGOVER_SWAB2"                               
## [856] "Perprotocol"                                  
## [857] "ph1.D15"                                      
## [858] "ph1.D29"                                      
## [859] "ph1.D92"                                      
## [860] "pre_study_booster_date"                       
## [861] "pre_study_booster_until_studydose1_day"       
## [862] "pre_study_booster_until_studydose1_day_median"
## [863] "pre_study_booster_until_studydose1_ind"       
## [864] "pre_study_infect_date"                        
## [865] "primary_booster_type"                         
## [866] "primary_vax1_date"                            
## [867] "primary_vax2_date"                            
## [868] "race"                                         
## [869] "RESULT"                                       
## [870] "RESULT_limit"                                 
## [871] "SCORCALL_SWAB1"                               
## [872] "SCORCALL_SWAB2"                               
## [873] "SCORVER_SWAB1"                                
## [874] "SCORVER_SWAB2"                                
## [875] "Sex"                                          
## [876] "SPKAADEL_SWAB1"                               
## [877] "SPKAADEL_SWAB2"                               
## [878] "SPKAAINS_SWAB1"                               
## [879] "SPKAAINS_SWAB2"                               
## [880] "SPKAASUB_SWAB1"                               
## [881] "SPKAASUB_SWAB2"                               
## [882] "stage"                                        
## [883] "State"                                        
## [884] "stratalab"                                    
## [885] "studydose1date"                               
## [886] "studydose2date"                               
## [887] "Subjectid"                                    
## [888] "symptm_infect1"                               
## [889] "symptm_infect1_date"                          
## [890] "symptm_infect1_date_imp"                      
## [891] "symptomatic_infect1"                          
## [892] "symptomatic_infect2"                          
## [893] "Target_study_day_numeric"                     
## [894] "TOTREADS_SWAB1"                               
## [895] "TOTREADS_SWAB2"                               
## [896] "treatment_actual"                             
## [897] "treatment_assigned"                           
## [898] "TrtA"                                         
## [899] "TrtB"                                         
## [900] "TrtC"                                         
## [901] "TrtmRNA"                                      
## [902] "TrtonedosemRNA"                               
## [903] "TrtSanofi"                                    
## [904] "TRUNCLIN_SWAB1"                               
## [905] "TRUNCLIN_SWAB2"                               
## [906] "TRUNCVER_SWAB1"                               
## [907] "TRUNCVER_SWAB2"                               
## [908] "UNITS"                                        
## [909] "Unknown"                                      
## [910] "White"
table(dat_mapped$treatment_actual, dat_mapped$stage)
##                                                 
##                                                    1   2   3   4
##   1 Dose Beta + Omicron (Moderna)                113   0   0   0
##   1 Dose Delta + Omicron (Moderna)               101   0   0   0
##   1 Dose Omicron (Moderna)                        99   0   0   0
##   1 Dose Omicron + Prototype (Moderna)            99   0   0   0
##   1 Dose Prototype (Moderna)                      99   0   0   0
##   2 Dose Beta + Omicron (Moderna)                 86   0   0   0
##   Beta (Pfizer 1)                                  0  51   0   0
##   Beta (Sanofi)                                    0   0  51   0
##   Beta + Omicron (Pfizer 1)                        0  52   0   0
##   Beta + Prototype (Sanofi)                        0   0  52   0
##   Beta + Wildtype/Prototype (Pfizer 1)             0  52   0   0
##   Omicron (Pfizer 1)                               0  54   0   0
##   Omicron + Wildtype/Prototype (Pfizer 1)          0  53   0   0
##   Omicron BA.1 + Wildtype/Prototype (Pfizer 2)     0   0   0 101
##   Omicron BA.4/5 + Wildtype/Prototype (Pfizer 2)   0   0   0 100
##   Prototype (Sanofi)                               0   0  49   0
##   Wildtype/Prototype (Pfizer 1)                    0  50   0   0
with(subset(dat, ph1.D15==1 & COVIDIndD22toD181), mytable(treatment_actual, COVIDlineageObserved))
##                                                 COVIDlineageObserved
## treatment_actual                                 FALSE TRUE
##   1 Dose Beta + Omicron (Moderna)                    9   28
##   1 Dose Delta + Omicron (Moderna)                   5   23
##   1 Dose Omicron (Moderna)                           7   18
##   1 Dose Omicron + Prototype (Moderna)               8   18
##   1 Dose Prototype (Moderna)                         7   20
##   Beta (Pfizer 1)                                    4    5
##   Beta + Omicron (Pfizer 1)                          3    4
##   Beta + Wildtype/Prototype (Pfizer 1)               2    7
##   Omicron (Pfizer 1)                                 5    3
##   Omicron + Wildtype/Prototype (Pfizer 1)            0    6
##   Omicron BA.1 + Wildtype/Prototype (Pfizer 2)       3    5
##   Omicron BA.4/5 + Wildtype/Prototype (Pfizer 2)     2    5
##   Wildtype/Prototype (Pfizer 1)                      4   12
table(dat_mapped$Immunemarkerset, dat_mapped$Perprotocol, useNA='ifany')
##    
##        0    1
##   0   26   24
##   1    0 1212
table(dat_mapped$Immunemarkerset, dat_mapped$eligibility_deviation, useNA='ifany')
##    
##             Y
##   0   47    3
##   1 1212    0